Discussion:
Error by pdb2gmx
(too old to reply)
Yanmei Song
2009-04-28 22:33:30 UTC
Permalink
Dear All users:

I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to the file in
order to make it as a GROMACS input pdb file. Then I can use pdb2gmx
to get the gro, itp and top file.

When I perform the pdb2gmx command, I got the error message:

Residue 'MOL' not found in residue topology database

Thank you in advance!

REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009
ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00
ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00
ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00
ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00
ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00
ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00
ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00
ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00
ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00
ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00
ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00
ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00
ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00
ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00
ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00
ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00
ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00
ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00
ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00
ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00
ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00
ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00
ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00
ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00
ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00
ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00
ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00
ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00
ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00
ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00
ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00
ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00
ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00
ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00
ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00
ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00
ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00
ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00
ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00
ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00
ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00
ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00
ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00
ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00
ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00
TER
--
Yanmei Song
Department of Chemical Engineering
ASU
Justin A. Lemkul
2009-04-28 22:37:04 UTC
Permalink
Post by Yanmei Song
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to the file in
order to make it as a GROMACS input pdb file. Then I can use pdb2gmx
to get the gro, itp and top file.
Residue 'MOL' not found in residue topology database
You can't expect pdb2gmx to be magic. A simple search of the list archives and
wiki will turn up the following:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

-Justin
Post by Yanmei Song
Thank you in advance!
REMARK Created: Tue Apr 28 15:02:20 US Mountain Standard Time 2009
ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00
ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00
ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00
ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00
ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00
ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00
ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00
ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00
ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00
ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00
ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00
ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00
ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00
ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00
ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00
ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00
ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00
ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00
ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00
ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00
ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00
ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00
ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00
ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00
ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00
ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00
ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00
ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00
ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00
ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00
ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00
ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00
ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00
ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00
ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00
ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00
ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00
ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00
ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00
ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00
ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00
ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00
ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00
ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00
ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00
TER
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Yanmei Song
2009-04-28 22:59:17 UTC
Permalink
Dear Justin:

Do you have any suggestions on how I can get the itp and gro file for
a very long polymer molecules (for example 500 united-atoms), which
only consists of Si, O and C atom. I can use PRODRG to generate a
short chain. But PRODRG has limitation of atom numbers in a molecule,
probably less than 300. So any ideas for building up a long chain
based on the short chain? By the way, I already have the force field
parameters.

Thanks a lot!
Post by Yanmei Song
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to the file in
order to make it as a GROMACS input pdb file. Then I can use pdb2gmx
to get the gro, itp and top file.
Residue 'MOL' not found in residue topology database
You can't expect pdb2gmx to be magic. ?A simple search of the list archives
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
-Justin
Post by Yanmei Song
Thank you in advance!
REMARK ? Created: ?Tue Apr 28 15:02:20 US Mountain Standard Time 2009
ATOM ? ? ?1 Si1 ?MOL A ? 1 ? ? ? 3.798 ? 2.502 ?-0.836 ?1.00 ?0.00
ATOM ? ? ?2 ?O2 ?MOL A ? 1 ? ? ? 4.664 ? 1.185 ?-0.027 ?1.00 ?0.00
ATOM ? ? ?3 Si4 ?MOL A ? 1 ? ? ? 4.900 ?-0.177 ? 1.079 ?1.00 ?0.00
ATOM ? ? ?4 ?O6 ?MOL A ? 1 ? ? ? 3.689 ?-1.438 ? 0.845 ?1.00 ?0.00
ATOM ? ? ?5 Si7 ?MOL A ? 1 ? ? ? 2.039 ?-2.056 ? 0.903 ?1.00 ?0.00
ATOM ? ? ?6 ?O8 ?MOL A ? 1 ? ? ? 2.039 ?-3.722 ? 0.332 ?1.00 ?0.00
ATOM ? ? ?7 Si9 ?MOL A ? 1 ? ? ? 1.180 ?-5.224 ? 0.014 ?1.00 ?0.00
ATOM ? ? ?8 ?O10 MOL A ? 1 ? ? ? 2.298 ?-6.420 ?-0.633 ?1.00 ?0.00
ATOM ? ? ?9 Si16 MOL A ? 1 ? ? ? 3.361 ?-7.028 ?-1.900 ?1.00 ?0.00
ATOM ? ? 10 ?O17 MOL A ? 1 ? ? ? 4.535 ?-5.799 ?-2.365 ?1.00 ?0.00
ATOM ? ? 11 Si18 MOL A ? 1 ? ? ? 5.953 ?-5.366 ?-3.320 ?1.00 ?0.00
ATOM ? ? 12 ?O22 MOL A ? 1 ? ? ? 6.258 ?-3.639 ?-3.185 ?1.00 ?0.00
ATOM ? ? 13 Si24 MOL A ? 1 ? ? ? 5.682 ?-1.999 ?-3.453 ?1.00 ?0.00
ATOM ? ? 14 ?O26 MOL A ? 1 ? ? ? 6.881 ?-0.844 ?-2.890 ?1.00 ?0.00
ATOM ? ? 15 Si28 MOL A ? 1 ? ? ? 8.517 ?-0.212 ?-3.003 ?1.00 ?0.00
ATOM ? ? 16 ?O29 MOL A ? 1 ? ? ? 8.809 ? 0.341 ?-4.647 ?1.00 ?0.00
ATOM ? ? 17 Si30 MOL A ? 1 ? ? ? 9.880 ? 1.056 ?-5.847 ?1.00 ?0.00
ATOM ? ? 18 ?C34 MOL A ? 1 ? ? ? 9.732 ?-1.565 ?-2.571 ?1.00 ?0.00
ATOM ? ? 19 ?C36 MOL A ? 1 ? ? ? 8.724 ? 1.219 ?-1.818 ?1.00 ?0.00
ATOM ? ? 20 ?C38 MOL A ? 1 ? ? ? 6.589 ?-0.910 ? 0.760 ?1.00 ?0.00
ATOM ? ? 21 ?C40 MOL A ? 1 ? ? ? 4.840 ? 0.411 ? 2.849 ?1.00 ?0.00
ATOM ? ? 22 ?C42 MOL A ? 1 ? ? ? 5.390 ?-1.733 ?-5.281 ?1.00 ?0.00
ATOM ? ? 23 ?C44 MOL A ? 1 ? ? ? 4.081 ?-1.754 ?-2.530 ?1.00 ?0.00
ATOM ? ? 24 ?C46 MOL A ? 1 ? ? ? 7.438 ?-6.318 ?-2.702 ?1.00 ?0.00
ATOM ? ? 25 ?C48 MOL A ? 1 ? ? ? 5.648 ?-5.792 ?-5.115 ?1.00 ?0.00
ATOM ? ? 26 ?C50 MOL A ? 1 ? ? ? 2.341 ?-7.493 ?-3.396 ?1.00 ?0.00
ATOM ? ? 27 ?C52 MOL A ? 1 ? ? ? 4.255 ?-8.543 ?-1.268 ?1.00 ?0.00
ATOM ? ? 28 ?C54 MOL A ? 1 ? ? ? 0.463 ?-5.865 ? 1.617 ?1.00 ?0.00
ATOM ? ? 29 ?C56 MOL A ? 1 ? ? ?-0.202 ?-4.925 ?-1.209 ?1.00 ?0.00
ATOM ? ? 30 ?C58 MOL A ? 1 ? ? ? 1.433 ?-2.009 ? 2.671 ?1.00 ?0.00
ATOM ? ? 31 ?C60 MOL A ? 1 ? ? ? 0.903 ?-1.026 ?-0.161 ?1.00 ?0.00
ATOM ? ? 32 ?O62 MOL A ? 1 ? ? ? 3.060 ? 3.615 ? 0.318 ?1.00 ?0.00
ATOM ? ? 33 Si63 MOL A ? 1 ? ? ? 1.891 ? 3.996 ? 1.583 ?1.00 ?0.00
ATOM ? ? 34 ?O64 MOL A ? 1 ? ? ? 2.107 ? 5.670 ? 2.078 ?1.00 ?0.00
ATOM ? ? 35 Si68 MOL A ? 1 ? ? ? 3.135 ? 6.928 ? 2.750 ?1.00 ?0.00
ATOM ? ? 36 ?C69 MOL A ? 1 ? ? ? 3.667 ? 6.449 ? 4.477 ?1.00 ?0.00
ATOM ? ? 37 ?C72 MOL A ? 1 ? ? ? 5.024 ? 3.447 ?-1.883 ?1.00 ?0.00
ATOM ? ? 38 ?C74 MOL A ? 1 ? ? ? 2.469 ? 1.818 ?-1.953 ?1.00 ?0.00
ATOM ? ? 39 ?C76 MOL A ? 1 ? ? ? 0.160 ? 3.770 ? 0.914 ?1.00 ?0.00
ATOM ? ? 40 ?C78 MOL A ? 1 ? ? ? 2.129 ? 2.878 ? 3.056 ?1.00 ?0.00
ATOM ? ? 41 ?C80 MOL A ? 1 ? ? ? 2.186 ? 8.538 ? 2.814 ?1.00 ?0.00
ATOM ? ? 42 Si84 MOL A ? 1 ? ? ? 4.912 ? 7.172 ? 1.476 ?1.00 ?0.00
ATOM ? ? 43 ?C84 MOL A ? 1 ? ? ? 8.985 ? 1.172 ?-7.484 ?1.00 ?0.00
ATOM ? ? 44 ?C86 MOL A ? 1 ? ? ?10.388 ? 2.767 ?-5.292 ?1.00 ?0.00
ATOM ? ? 45 ?C88 MOL A ? 1 ? ? ?11.402 ?-0.013 ?-6.044 ?1.00 ?0.00
TER
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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--
Yanmei Song
Department of Chemical Engineering
ASU
Dallas B. Warren
2009-04-28 23:03:49 UTC
Permalink
If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Wednesday, 29 April 2009 8:59 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Do you have any suggestions on how I can get the itp and gro file for
a very long polymer molecules (for example 500 united-atoms), which
only consists of Si, O and C atom. I can use PRODRG to generate a
short chain. But PRODRG has limitation of atom numbers in a molecule,
probably less than 300. So any ideas for building up a long chain
based on the short chain? By the way, I already have the force field
parameters.
Thanks a lot!
On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul
Post by Yanmei Song
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to
the file in
Post by Yanmei Song
order to make it as a GROMACS input pdb file. Then I can
use pdb2gmx
Post by Yanmei Song
to get the gro, itp and top file.
Residue 'MOL' not found in residue topology database
You can't expect pdb2gmx to be magic. ?A simple search of
the list archives
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not
_found_in_residue_topology_database
-Justin
Post by Yanmei Song
Thank you in advance!
REMARK ? Created: ?Tue Apr 28 15:02:20 US Mountain
Standard Time 2009
Post by Yanmei Song
ATOM ? ? ?1 Si1 ?MOL A ? 1 ? ? ? 3.798 ? 2.502 ?-0.836 ?1.00 ?0.00
ATOM ? ? ?2 ?O2 ?MOL A ? 1 ? ? ? 4.664 ? 1.185 ?-0.027 ?1.00 ?0.00
ATOM ? ? ?3 Si4 ?MOL A ? 1 ? ? ? 4.900 ?-0.177 ? 1.079 ?1.00 ?0.00
ATOM ? ? ?4 ?O6 ?MOL A ? 1 ? ? ? 3.689 ?-1.438 ? 0.845 ?1.00 ?0.00
ATOM ? ? ?5 Si7 ?MOL A ? 1 ? ? ? 2.039 ?-2.056 ? 0.903 ?1.00 ?0.00
ATOM ? ? ?6 ?O8 ?MOL A ? 1 ? ? ? 2.039 ?-3.722 ? 0.332 ?1.00 ?0.00
ATOM ? ? ?7 Si9 ?MOL A ? 1 ? ? ? 1.180 ?-5.224 ? 0.014 ?1.00 ?0.00
ATOM ? ? ?8 ?O10 MOL A ? 1 ? ? ? 2.298 ?-6.420 ?-0.633 ?1.00 ?0.00
ATOM ? ? ?9 Si16 MOL A ? 1 ? ? ? 3.361 ?-7.028 ?-1.900 ?1.00 ?0.00
ATOM ? ? 10 ?O17 MOL A ? 1 ? ? ? 4.535 ?-5.799 ?-2.365 ?1.00 ?0.00
ATOM ? ? 11 Si18 MOL A ? 1 ? ? ? 5.953 ?-5.366 ?-3.320 ?1.00 ?0.00
ATOM ? ? 12 ?O22 MOL A ? 1 ? ? ? 6.258 ?-3.639 ?-3.185 ?1.00 ?0.00
ATOM ? ? 13 Si24 MOL A ? 1 ? ? ? 5.682 ?-1.999 ?-3.453 ?1.00 ?0.00
ATOM ? ? 14 ?O26 MOL A ? 1 ? ? ? 6.881 ?-0.844 ?-2.890 ?1.00 ?0.00
ATOM ? ? 15 Si28 MOL A ? 1 ? ? ? 8.517 ?-0.212 ?-3.003 ?1.00 ?0.00
ATOM ? ? 16 ?O29 MOL A ? 1 ? ? ? 8.809 ? 0.341 ?-4.647 ?1.00 ?0.00
ATOM ? ? 17 Si30 MOL A ? 1 ? ? ? 9.880 ? 1.056 ?-5.847 ?1.00 ?0.00
ATOM ? ? 18 ?C34 MOL A ? 1 ? ? ? 9.732 ?-1.565 ?-2.571 ?1.00 ?0.00
ATOM ? ? 19 ?C36 MOL A ? 1 ? ? ? 8.724 ? 1.219 ?-1.818 ?1.00 ?0.00
ATOM ? ? 20 ?C38 MOL A ? 1 ? ? ? 6.589 ?-0.910 ? 0.760 ?1.00 ?0.00
ATOM ? ? 21 ?C40 MOL A ? 1 ? ? ? 4.840 ? 0.411 ? 2.849 ?1.00 ?0.00
ATOM ? ? 22 ?C42 MOL A ? 1 ? ? ? 5.390 ?-1.733 ?-5.281 ?1.00 ?0.00
ATOM ? ? 23 ?C44 MOL A ? 1 ? ? ? 4.081 ?-1.754 ?-2.530 ?1.00 ?0.00
ATOM ? ? 24 ?C46 MOL A ? 1 ? ? ? 7.438 ?-6.318 ?-2.702 ?1.00 ?0.00
ATOM ? ? 25 ?C48 MOL A ? 1 ? ? ? 5.648 ?-5.792 ?-5.115 ?1.00 ?0.00
ATOM ? ? 26 ?C50 MOL A ? 1 ? ? ? 2.341 ?-7.493 ?-3.396 ?1.00 ?0.00
ATOM ? ? 27 ?C52 MOL A ? 1 ? ? ? 4.255 ?-8.543 ?-1.268 ?1.00 ?0.00
ATOM ? ? 28 ?C54 MOL A ? 1 ? ? ? 0.463 ?-5.865 ? 1.617 ?1.00 ?0.00
ATOM ? ? 29 ?C56 MOL A ? 1 ? ? ?-0.202 ?-4.925 ?-1.209 ?1.00 ?0.00
ATOM ? ? 30 ?C58 MOL A ? 1 ? ? ? 1.433 ?-2.009 ? 2.671 ?1.00 ?0.00
ATOM ? ? 31 ?C60 MOL A ? 1 ? ? ? 0.903 ?-1.026 ?-0.161 ?1.00 ?0.00
ATOM ? ? 32 ?O62 MOL A ? 1 ? ? ? 3.060 ? 3.615 ? 0.318 ?1.00 ?0.00
ATOM ? ? 33 Si63 MOL A ? 1 ? ? ? 1.891 ? 3.996 ? 1.583 ?1.00 ?0.00
ATOM ? ? 34 ?O64 MOL A ? 1 ? ? ? 2.107 ? 5.670 ? 2.078 ?1.00 ?0.00
ATOM ? ? 35 Si68 MOL A ? 1 ? ? ? 3.135 ? 6.928 ? 2.750 ?1.00 ?0.00
ATOM ? ? 36 ?C69 MOL A ? 1 ? ? ? 3.667 ? 6.449 ? 4.477 ?1.00 ?0.00
ATOM ? ? 37 ?C72 MOL A ? 1 ? ? ? 5.024 ? 3.447 ?-1.883 ?1.00 ?0.00
ATOM ? ? 38 ?C74 MOL A ? 1 ? ? ? 2.469 ? 1.818 ?-1.953 ?1.00 ?0.00
ATOM ? ? 39 ?C76 MOL A ? 1 ? ? ? 0.160 ? 3.770 ? 0.914 ?1.00 ?0.00
ATOM ? ? 40 ?C78 MOL A ? 1 ? ? ? 2.129 ? 2.878 ? 3.056 ?1.00 ?0.00
ATOM ? ? 41 ?C80 MOL A ? 1 ? ? ? 2.186 ? 8.538 ? 2.814 ?1.00 ?0.00
ATOM ? ? 42 Si84 MOL A ? 1 ? ? ? 4.912 ? 7.172 ? 1.476 ?1.00 ?0.00
ATOM ? ? 43 ?C84 MOL A ? 1 ? ? ? 8.985 ? 1.172 ?-7.484 ?1.00 ?0.00
ATOM ? ? 44 ?C86 MOL A ? 1 ? ? ?10.388 ? 2.767 ?-5.292 ?1.00 ?0.00
ATOM ? ? 45 ?C88 MOL A ? 1 ? ? ?11.402 ?-0.013 ?-6.044 ?1.00 ?0.00
TER
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
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the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
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Please search the archive at http://www.gromacs.org/search
before posting!
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Yanmei Song
2009-04-28 23:23:44 UTC
Permalink
Dear Dallas:

Thanks for your response. It consists of many repeating units. Do you
mean I can write the rtp entry for one repeating unit and give it a
residue name. After that I need to insert this into the force field
rtp file, right? How can I do that? It seems I can not change the rtp
file. Thanks.

On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren
Post by Dallas B. Warren
If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Wednesday, 29 April 2009 8:59 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Do you have any suggestions on how I can get the itp and gro file for
a very long polymer molecules (for example 500 united-atoms), which
only consists of Si, O and C atom. I can use PRODRG to generate a
short chain. But PRODRG has limitation of atom numbers in a molecule,
probably less than 300. So any ideas for building up a long chain
based on the short chain? By the way, I already have the force field
parameters.
Thanks a lot!
On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul
Post by Yanmei Song
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to
the file in
Post by Yanmei Song
order to make it as a GROMACS input pdb file. Then I can
use pdb2gmx
Post by Yanmei Song
to get the gro, itp and top file.
Residue 'MOL' not found in residue topology database
You can't expect pdb2gmx to be magic. ?A simple search of
the list archives
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not
_found_in_residue_topology_database
-Justin
Post by Yanmei Song
Thank you in advance!
REMARK ? Created: ?Tue Apr 28 15:02:20 US Mountain
Standard Time 2009
Post by Yanmei Song
ATOM ? ? ?1 Si1 ?MOL A ? 1 ? ? ? 3.798 ? 2.502 ?-0.836 ?1.00 ?0.00
ATOM ? ? ?2 ?O2 ?MOL A ? 1 ? ? ? 4.664 ? 1.185 ?-0.027 ?1.00 ?0.00
ATOM ? ? ?3 Si4 ?MOL A ? 1 ? ? ? 4.900 ?-0.177 ? 1.079 ?1.00 ?0.00
ATOM ? ? ?4 ?O6 ?MOL A ? 1 ? ? ? 3.689 ?-1.438 ? 0.845 ?1.00 ?0.00
ATOM ? ? ?5 Si7 ?MOL A ? 1 ? ? ? 2.039 ?-2.056 ? 0.903 ?1.00 ?0.00
ATOM ? ? ?6 ?O8 ?MOL A ? 1 ? ? ? 2.039 ?-3.722 ? 0.332 ?1.00 ?0.00
ATOM ? ? ?7 Si9 ?MOL A ? 1 ? ? ? 1.180 ?-5.224 ? 0.014 ?1.00 ?0.00
ATOM ? ? ?8 ?O10 MOL A ? 1 ? ? ? 2.298 ?-6.420 ?-0.633 ?1.00 ?0.00
ATOM ? ? ?9 Si16 MOL A ? 1 ? ? ? 3.361 ?-7.028 ?-1.900 ?1.00 ?0.00
ATOM ? ? 10 ?O17 MOL A ? 1 ? ? ? 4.535 ?-5.799 ?-2.365 ?1.00 ?0.00
ATOM ? ? 11 Si18 MOL A ? 1 ? ? ? 5.953 ?-5.366 ?-3.320 ?1.00 ?0.00
ATOM ? ? 12 ?O22 MOL A ? 1 ? ? ? 6.258 ?-3.639 ?-3.185 ?1.00 ?0.00
ATOM ? ? 13 Si24 MOL A ? 1 ? ? ? 5.682 ?-1.999 ?-3.453 ?1.00 ?0.00
ATOM ? ? 14 ?O26 MOL A ? 1 ? ? ? 6.881 ?-0.844 ?-2.890 ?1.00 ?0.00
ATOM ? ? 15 Si28 MOL A ? 1 ? ? ? 8.517 ?-0.212 ?-3.003 ?1.00 ?0.00
ATOM ? ? 16 ?O29 MOL A ? 1 ? ? ? 8.809 ? 0.341 ?-4.647 ?1.00 ?0.00
ATOM ? ? 17 Si30 MOL A ? 1 ? ? ? 9.880 ? 1.056 ?-5.847 ?1.00 ?0.00
ATOM ? ? 18 ?C34 MOL A ? 1 ? ? ? 9.732 ?-1.565 ?-2.571 ?1.00 ?0.00
ATOM ? ? 19 ?C36 MOL A ? 1 ? ? ? 8.724 ? 1.219 ?-1.818 ?1.00 ?0.00
ATOM ? ? 20 ?C38 MOL A ? 1 ? ? ? 6.589 ?-0.910 ? 0.760 ?1.00 ?0.00
ATOM ? ? 21 ?C40 MOL A ? 1 ? ? ? 4.840 ? 0.411 ? 2.849 ?1.00 ?0.00
ATOM ? ? 22 ?C42 MOL A ? 1 ? ? ? 5.390 ?-1.733 ?-5.281 ?1.00 ?0.00
ATOM ? ? 23 ?C44 MOL A ? 1 ? ? ? 4.081 ?-1.754 ?-2.530 ?1.00 ?0.00
ATOM ? ? 24 ?C46 MOL A ? 1 ? ? ? 7.438 ?-6.318 ?-2.702 ?1.00 ?0.00
ATOM ? ? 25 ?C48 MOL A ? 1 ? ? ? 5.648 ?-5.792 ?-5.115 ?1.00 ?0.00
ATOM ? ? 26 ?C50 MOL A ? 1 ? ? ? 2.341 ?-7.493 ?-3.396 ?1.00 ?0.00
ATOM ? ? 27 ?C52 MOL A ? 1 ? ? ? 4.255 ?-8.543 ?-1.268 ?1.00 ?0.00
ATOM ? ? 28 ?C54 MOL A ? 1 ? ? ? 0.463 ?-5.865 ? 1.617 ?1.00 ?0.00
ATOM ? ? 29 ?C56 MOL A ? 1 ? ? ?-0.202 ?-4.925 ?-1.209 ?1.00 ?0.00
ATOM ? ? 30 ?C58 MOL A ? 1 ? ? ? 1.433 ?-2.009 ? 2.671 ?1.00 ?0.00
ATOM ? ? 31 ?C60 MOL A ? 1 ? ? ? 0.903 ?-1.026 ?-0.161 ?1.00 ?0.00
ATOM ? ? 32 ?O62 MOL A ? 1 ? ? ? 3.060 ? 3.615 ? 0.318 ?1.00 ?0.00
ATOM ? ? 33 Si63 MOL A ? 1 ? ? ? 1.891 ? 3.996 ? 1.583 ?1.00 ?0.00
ATOM ? ? 34 ?O64 MOL A ? 1 ? ? ? 2.107 ? 5.670 ? 2.078 ?1.00 ?0.00
ATOM ? ? 35 Si68 MOL A ? 1 ? ? ? 3.135 ? 6.928 ? 2.750 ?1.00 ?0.00
ATOM ? ? 36 ?C69 MOL A ? 1 ? ? ? 3.667 ? 6.449 ? 4.477 ?1.00 ?0.00
ATOM ? ? 37 ?C72 MOL A ? 1 ? ? ? 5.024 ? 3.447 ?-1.883 ?1.00 ?0.00
ATOM ? ? 38 ?C74 MOL A ? 1 ? ? ? 2.469 ? 1.818 ?-1.953 ?1.00 ?0.00
ATOM ? ? 39 ?C76 MOL A ? 1 ? ? ? 0.160 ? 3.770 ? 0.914 ?1.00 ?0.00
ATOM ? ? 40 ?C78 MOL A ? 1 ? ? ? 2.129 ? 2.878 ? 3.056 ?1.00 ?0.00
ATOM ? ? 41 ?C80 MOL A ? 1 ? ? ? 2.186 ? 8.538 ? 2.814 ?1.00 ?0.00
ATOM ? ? 42 Si84 MOL A ? 1 ? ? ? 4.912 ? 7.172 ? 1.476 ?1.00 ?0.00
ATOM ? ? 43 ?C84 MOL A ? 1 ? ? ? 8.985 ? 1.172 ?-7.484 ?1.00 ?0.00
ATOM ? ? 44 ?C86 MOL A ? 1 ? ? ?10.388 ? 2.767 ?-5.292 ?1.00 ?0.00
ATOM ? ? 45 ?C88 MOL A ? 1 ? ? ?11.402 ?-0.013 ?-6.044 ?1.00 ?0.00
TER
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use
the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
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Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
Justin A. Lemkul
2009-04-28 23:28:44 UTC
Permalink
Post by Yanmei Song
Thanks for your response. It consists of many repeating units. Do you
mean I can write the rtp entry for one repeating unit and give it a
residue name. After that I need to insert this into the force field
rtp file, right? How can I do that? It seems I can not change the rtp
file. Thanks.
You will need an entry for the repeat units and the terminal/capping groups.
You can make a local copy of the .rtp file and edit it in your working
directory; pdb2gmx will then read this copy when processing your structure.

-Justin
Post by Yanmei Song
On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren
Post by Dallas B. Warren
If it is a repeating unit, then you can build a .rtp entry then use it as you would for a protein.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Wednesday, 29 April 2009 8:59 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Do you have any suggestions on how I can get the itp and gro file for
a very long polymer molecules (for example 500 united-atoms), which
only consists of Si, O and C atom. I can use PRODRG to generate a
short chain. But PRODRG has limitation of atom numbers in a molecule,
probably less than 300. So any ideas for building up a long chain
based on the short chain? By the way, I already have the force field
parameters.
Thanks a lot!
On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to
the file in
Post by Justin A. Lemkul
Post by Yanmei Song
order to make it as a GROMACS input pdb file. Then I can
use pdb2gmx
Post by Justin A. Lemkul
Post by Yanmei Song
to get the gro, itp and top file.
Residue 'MOL' not found in residue topology database
You can't expect pdb2gmx to be magic. A simple search of
the list archives
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not
_found_in_residue_topology_database
Post by Justin A. Lemkul
-Justin
Post by Yanmei Song
Thank you in advance!
REMARK Created: Tue Apr 28 15:02:20 US Mountain
Standard Time 2009
Post by Justin A. Lemkul
Post by Yanmei Song
ATOM 1 Si1 MOL A 1 3.798 2.502 -0.836 1.00 0.00
ATOM 2 O2 MOL A 1 4.664 1.185 -0.027 1.00 0.00
ATOM 3 Si4 MOL A 1 4.900 -0.177 1.079 1.00 0.00
ATOM 4 O6 MOL A 1 3.689 -1.438 0.845 1.00 0.00
ATOM 5 Si7 MOL A 1 2.039 -2.056 0.903 1.00 0.00
ATOM 6 O8 MOL A 1 2.039 -3.722 0.332 1.00 0.00
ATOM 7 Si9 MOL A 1 1.180 -5.224 0.014 1.00 0.00
ATOM 8 O10 MOL A 1 2.298 -6.420 -0.633 1.00 0.00
ATOM 9 Si16 MOL A 1 3.361 -7.028 -1.900 1.00 0.00
ATOM 10 O17 MOL A 1 4.535 -5.799 -2.365 1.00 0.00
ATOM 11 Si18 MOL A 1 5.953 -5.366 -3.320 1.00 0.00
ATOM 12 O22 MOL A 1 6.258 -3.639 -3.185 1.00 0.00
ATOM 13 Si24 MOL A 1 5.682 -1.999 -3.453 1.00 0.00
ATOM 14 O26 MOL A 1 6.881 -0.844 -2.890 1.00 0.00
ATOM 15 Si28 MOL A 1 8.517 -0.212 -3.003 1.00 0.00
ATOM 16 O29 MOL A 1 8.809 0.341 -4.647 1.00 0.00
ATOM 17 Si30 MOL A 1 9.880 1.056 -5.847 1.00 0.00
ATOM 18 C34 MOL A 1 9.732 -1.565 -2.571 1.00 0.00
ATOM 19 C36 MOL A 1 8.724 1.219 -1.818 1.00 0.00
ATOM 20 C38 MOL A 1 6.589 -0.910 0.760 1.00 0.00
ATOM 21 C40 MOL A 1 4.840 0.411 2.849 1.00 0.00
ATOM 22 C42 MOL A 1 5.390 -1.733 -5.281 1.00 0.00
ATOM 23 C44 MOL A 1 4.081 -1.754 -2.530 1.00 0.00
ATOM 24 C46 MOL A 1 7.438 -6.318 -2.702 1.00 0.00
ATOM 25 C48 MOL A 1 5.648 -5.792 -5.115 1.00 0.00
ATOM 26 C50 MOL A 1 2.341 -7.493 -3.396 1.00 0.00
ATOM 27 C52 MOL A 1 4.255 -8.543 -1.268 1.00 0.00
ATOM 28 C54 MOL A 1 0.463 -5.865 1.617 1.00 0.00
ATOM 29 C56 MOL A 1 -0.202 -4.925 -1.209 1.00 0.00
ATOM 30 C58 MOL A 1 1.433 -2.009 2.671 1.00 0.00
ATOM 31 C60 MOL A 1 0.903 -1.026 -0.161 1.00 0.00
ATOM 32 O62 MOL A 1 3.060 3.615 0.318 1.00 0.00
ATOM 33 Si63 MOL A 1 1.891 3.996 1.583 1.00 0.00
ATOM 34 O64 MOL A 1 2.107 5.670 2.078 1.00 0.00
ATOM 35 Si68 MOL A 1 3.135 6.928 2.750 1.00 0.00
ATOM 36 C69 MOL A 1 3.667 6.449 4.477 1.00 0.00
ATOM 37 C72 MOL A 1 5.024 3.447 -1.883 1.00 0.00
ATOM 38 C74 MOL A 1 2.469 1.818 -1.953 1.00 0.00
ATOM 39 C76 MOL A 1 0.160 3.770 0.914 1.00 0.00
ATOM 40 C78 MOL A 1 2.129 2.878 3.056 1.00 0.00
ATOM 41 C80 MOL A 1 2.186 8.538 2.814 1.00 0.00
ATOM 42 Si84 MOL A 1 4.912 7.172 1.476 1.00 0.00
ATOM 43 C84 MOL A 1 8.985 1.172 -7.484 1.00 0.00
ATOM 44 C86 MOL A 1 10.388 2.767 -5.292 1.00 0.00
ATOM 45 C88 MOL A 1 11.402 -0.013 -6.044 1.00 0.00
TER
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Dallas B. Warren
2009-04-28 23:38:15 UTC
Permalink
That is correct. Fact you can't edit the .rtp file is based on your local computer system permissions. Normally, best idea is to make your own changes to a local copy, and use that.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Wednesday, 29 April 2009 9:24 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Thanks for your response. It consists of many repeating units. Do you
mean I can write the rtp entry for one repeating unit and give it a
residue name. After that I need to insert this into the force field
rtp file, right? How can I do that? It seems I can not change the rtp
file. Thanks.
On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren
Post by Dallas B. Warren
If it is a repeating unit, then you can build a .rtp entry
then use it as you would for a protein.
Post by Dallas B. Warren
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem
begins to resemble a nail.
Post by Dallas B. Warren
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Wednesday, 29 April 2009 8:59 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Do you have any suggestions on how I can get the itp and
gro file for
Post by Dallas B. Warren
a very long polymer molecules (for example 500 united-atoms), which
only consists of Si, O and C atom. I can use PRODRG to generate a
short chain. But PRODRG has limitation of atom numbers in
a molecule,
Post by Dallas B. Warren
probably less than 300. So any ideas for building up a long chain
based on the short chain? By the way, I already have the
force field
Post by Dallas B. Warren
parameters.
Thanks a lot!
On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul
Post by Yanmei Song
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to
the file in
Post by Yanmei Song
order to make it as a GROMACS input pdb file. Then I can
use pdb2gmx
Post by Yanmei Song
to get the gro, itp and top file.
Residue 'MOL' not found in residue topology database
You can't expect pdb2gmx to be magic. ?A simple search of
the list archives
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not
_found_in_residue_topology_database
-Justin
Post by Yanmei Song
Thank you in advance!
REMARK ? Created: ?Tue Apr 28 15:02:20 US Mountain
Standard Time 2009
Post by Yanmei Song
ATOM ? ? ?1 Si1 ?MOL A ? 1 ? ? ? 3.798 ? 2.502 ?-0.836 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?2 ?O2 ?MOL A ? 1 ? ? ? 4.664 ? 1.185 ?-0.027 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?3 Si4 ?MOL A ? 1 ? ? ? 4.900 ?-0.177 ? 1.079 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?4 ?O6 ?MOL A ? 1 ? ? ? 3.689 ?-1.438 ? 0.845 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?5 Si7 ?MOL A ? 1 ? ? ? 2.039 ?-2.056 ? 0.903 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?6 ?O8 ?MOL A ? 1 ? ? ? 2.039 ?-3.722 ? 0.332 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?7 Si9 ?MOL A ? 1 ? ? ? 1.180 ?-5.224 ? 0.014 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?8 ?O10 MOL A ? 1 ? ? ? 2.298 ?-6.420 ?-0.633 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?9 Si16 MOL A ? 1 ? ? ? 3.361 ?-7.028 ?-1.900 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 10 ?O17 MOL A ? 1 ? ? ? 4.535 ?-5.799 ?-2.365 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 11 Si18 MOL A ? 1 ? ? ? 5.953 ?-5.366 ?-3.320 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 12 ?O22 MOL A ? 1 ? ? ? 6.258 ?-3.639 ?-3.185 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 13 Si24 MOL A ? 1 ? ? ? 5.682 ?-1.999 ?-3.453 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 14 ?O26 MOL A ? 1 ? ? ? 6.881 ?-0.844 ?-2.890 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 15 Si28 MOL A ? 1 ? ? ? 8.517 ?-0.212 ?-3.003 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 16 ?O29 MOL A ? 1 ? ? ? 8.809 ? 0.341 ?-4.647 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 17 Si30 MOL A ? 1 ? ? ? 9.880 ? 1.056 ?-5.847 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 18 ?C34 MOL A ? 1 ? ? ? 9.732 ?-1.565 ?-2.571 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 19 ?C36 MOL A ? 1 ? ? ? 8.724 ? 1.219 ?-1.818 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 20 ?C38 MOL A ? 1 ? ? ? 6.589 ?-0.910 ? 0.760 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 21 ?C40 MOL A ? 1 ? ? ? 4.840 ? 0.411 ? 2.849 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 22 ?C42 MOL A ? 1 ? ? ? 5.390 ?-1.733 ?-5.281 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 23 ?C44 MOL A ? 1 ? ? ? 4.081 ?-1.754 ?-2.530 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 24 ?C46 MOL A ? 1 ? ? ? 7.438 ?-6.318 ?-2.702 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 25 ?C48 MOL A ? 1 ? ? ? 5.648 ?-5.792 ?-5.115 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 26 ?C50 MOL A ? 1 ? ? ? 2.341 ?-7.493 ?-3.396 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 27 ?C52 MOL A ? 1 ? ? ? 4.255 ?-8.543 ?-1.268 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 28 ?C54 MOL A ? 1 ? ? ? 0.463 ?-5.865 ? 1.617 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 29 ?C56 MOL A ? 1 ? ? ?-0.202 ?-4.925 ?-1.209 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 30 ?C58 MOL A ? 1 ? ? ? 1.433 ?-2.009 ? 2.671 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 31 ?C60 MOL A ? 1 ? ? ? 0.903 ?-1.026 ?-0.161 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 32 ?O62 MOL A ? 1 ? ? ? 3.060 ? 3.615 ? 0.318 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 33 Si63 MOL A ? 1 ? ? ? 1.891 ? 3.996 ? 1.583 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 34 ?O64 MOL A ? 1 ? ? ? 2.107 ? 5.670 ? 2.078 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 35 Si68 MOL A ? 1 ? ? ? 3.135 ? 6.928 ? 2.750 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 36 ?C69 MOL A ? 1 ? ? ? 3.667 ? 6.449 ? 4.477 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 37 ?C72 MOL A ? 1 ? ? ? 5.024 ? 3.447 ?-1.883 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 38 ?C74 MOL A ? 1 ? ? ? 2.469 ? 1.818 ?-1.953 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 39 ?C76 MOL A ? 1 ? ? ? 0.160 ? 3.770 ? 0.914 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 40 ?C78 MOL A ? 1 ? ? ? 2.129 ? 2.878 ? 3.056 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 41 ?C80 MOL A ? 1 ? ? ? 2.186 ? 8.538 ? 2.814 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 42 Si84 MOL A ? 1 ? ? ? 4.912 ? 7.172 ? 1.476 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 43 ?C84 MOL A ? 1 ? ? ? 8.985 ? 1.172 ?-7.484 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 44 ?C86 MOL A ? 1 ? ? ?10.388 ? 2.767 ?-5.292 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 45 ?C88 MOL A ? 1 ? ? ?11.402 ?-0.013 ?-6.044 ?
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
TER
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Yanmei Song
Department of Chemical Engineering
ASU
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Post by Dallas B. Warren
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Yanmei Song
Department of Chemical Engineering
ASU
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Yanmei Song
2009-04-29 22:50:00 UTC
Permalink
Dear Justin and Dallas:

Thank you for your help earlier.

I made a copy of ffoplsaa.rtp to my working directory and add a new
residue to it. Then perform the following command:

pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp

Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat

Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43b1 vacuum force field
2: GROMOS96 43a2 force field (improved alkane dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: Encad all-atom force field, using scaled-down vacuum charges
8: Encad all-atom force field, using full solvent charges
6
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms

chain #res #atoms
1 'A' 1 45

All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp

-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289

Fatal error:
in .rtp file at line:


-------------------------------------------------------
And also my pdb file:

ATOM 1 Si1 PDM A 1 3.796 2.499 -0.834 1.00 0.00
ATOM 2 O2 PDM A 1 4.661 1.181 -0.025 1.00 0.00
ATOM 3 Si4 PDM A 1 4.896 -0.181 1.082 1.00 0.00
ATOM 4 O6 PDM A 1 3.686 -1.442 0.846 1.00 0.00
ATOM 5 Si7 PDM A 1 2.036 -2.061 0.903 1.00 0.00
ATOM 6 O8 PDM A 1 2.038 -3.727 0.331 1.00 0.00
ATOM 7 Si9 PDM A 1 1.180 -5.229 0.010 1.00 0.00
ATOM 8 O10 PDM A 1 2.299 -6.424 -0.637 1.00 0.00
ATOM 9 Si16 PDM A 1 3.364 -7.030 -1.904 1.00 0.00
ATOM 10 O17 PDM A 1 4.537 -5.799 -2.367 1.00 0.00
ATOM 11 Si18 PDM A 1 5.956 -5.364 -3.320 1.00 0.00
ATOM 12 O22 PDM A 1 6.259 -3.637 -3.183 1.00 0.00
ATOM 13 Si24 PDM A 1 5.682 -1.997 -3.451 1.00 0.00
ATOM 14 O26 PDM A 1 6.879 -0.842 -2.885 1.00 0.00
ATOM 15 Si28 PDM A 1 8.515 -0.209 -2.996 1.00 0.00
ATOM 16 O29 PDM A 1 8.808 0.346 -4.640 1.00 0.00
ATOM 17 Si30 PDM A 1 9.879 1.063 -5.838 1.00 0.00
ATOM 18 C34 PDM A 1 9.731 -1.561 -2.566 1.00 0.00
ATOM 19 C36 PDM A 1 8.720 1.221 -1.809 1.00 0.00
ATOM 20 C38 PDM A 1 6.585 -0.914 0.764 1.00 0.00
ATOM 21 C40 PDM A 1 4.835 0.406 2.852 1.00 0.00
ATOM 22 C42 PDM A 1 5.391 -1.730 -5.278 1.00 0.00
ATOM 23 C44 PDM A 1 4.080 -1.754 -2.529 1.00 0.00
ATOM 24 C46 PDM A 1 7.441 -6.315 -2.701 1.00 0.00
ATOM 25 C48 PDM A 1 5.652 -5.789 -5.115 1.00 0.00
ATOM 26 C50 PDM A 1 2.345 -7.495 -3.401 1.00 0.00
ATOM 27 C52 PDM A 1 4.259 -8.545 -1.272 1.00 0.00
ATOM 28 C54 PDM A 1 0.462 -5.872 1.612 1.00 0.00
ATOM 29 C56 PDM A 1 -0.201 -4.930 -1.214 1.00 0.00
ATOM 30 C58 PDM A 1 1.428 -2.016 2.670 1.00 0.00
ATOM 31 C60 PDM A 1 0.900 -1.032 -0.161 1.00 0.00
ATOM 32 O62 PDM A 1 3.063 3.615 0.320 1.00 0.00
ATOM 33 Si63 PDM A 1 1.897 4.001 1.587 1.00 0.00
ATOM 34 O64 PDM A 1 2.116 5.675 2.077 1.00 0.00
ATOM 35 Si68 PDM A 1 3.148 6.934 2.744 1.00 0.00
ATOM 36 C69 PDM A 1 3.682 6.458 4.471 1.00 0.00
ATOM 37 C72 PDM A 1 5.023 3.440 -1.884 1.00 0.00
ATOM 38 C74 PDM A 1 2.464 1.816 -1.948 1.00 0.00
ATOM 39 C76 PDM A 1 0.164 3.775 0.923 1.00 0.00
ATOM 40 C78 PDM A 1 2.137 2.886 3.063 1.00 0.00
ATOM 41 C80 PDM A 1 2.202 8.545 2.805 1.00 0.00
ATOM 42 Si84 PDM A 1 4.922 7.171 1.466 1.00 0.00
ATOM 43 C84 PDM A 1 8.984 1.182 -7.476 1.00 0.00
ATOM 44 C86 PDM A 1 10.387 2.774 -5.280 1.00 0.00
ATOM 45 C88 PDM A 1 11.401 -0.004 -6.037 1.00 0.00
TER

Do you have any idea what I did wrong? It seems the GROMACS doesn't
give the wrong line by
Fatal error:
in .rtp file at line:
-------------------------------------------------------
Thank you so much for your help in advance!


On Tue, Apr 28, 2009 at 4:38 PM, Dallas B. Warren
That is correct. ?Fact you can't edit the .rtp file is based on your local computer system permissions. ?Normally, best idea is to make your own changes to a local copy, and use that.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Wednesday, 29 April 2009 9:24 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Thanks for your response. It consists of many repeating units. Do you
mean I can write the rtp entry for one repeating unit and give it a
residue name. After that I need to insert this into the force field
rtp file, right? How can I do that? It seems I can not change the rtp
file. ?Thanks.
On Tue, Apr 28, 2009 at 4:03 PM, Dallas B. Warren
Post by Dallas B. Warren
If it is a repeating unit, then you can build a .rtp entry
then use it as you would for a protein.
Post by Dallas B. Warren
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem
begins to resemble a nail.
Post by Dallas B. Warren
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Wednesday, 29 April 2009 8:59 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
Do you have any suggestions on how I can get the itp and
gro file for
Post by Dallas B. Warren
a very long polymer molecules (for example 500 united-atoms), which
only consists of Si, O and C atom. I can use PRODRG to generate a
short chain. But PRODRG has limitation of atom numbers in
a molecule,
Post by Dallas B. Warren
probably less than 300. So any ideas for building up a long chain
based on the short chain? By the way, I already have the
force field
Post by Dallas B. Warren
parameters.
Thanks a lot!
On Tue, Apr 28, 2009 at 3:37 PM, Justin A. Lemkul
Post by Yanmei Song
I was trying to set up a long chain polymer system. I got the
following PDB file from WebLab. How can I make changes to
the file in
Post by Yanmei Song
order to make it as a GROMACS input pdb file. Then I can
use pdb2gmx
Post by Yanmei Song
to get the gro, itp and top file.
Residue 'MOL' not found in residue topology database
You can't expect pdb2gmx to be magic. ?A simple search of
the list archives
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not
_found_in_residue_topology_database
-Justin
Post by Yanmei Song
Thank you in advance!
REMARK ? Created: ?Tue Apr 28 15:02:20 US Mountain
Standard Time 2009
Post by Yanmei Song
ATOM ? ? ?1 Si1 ?MOL A ? 1 ? ? ? 3.798 ? 2.502 ?-0.836
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?2 ?O2 ?MOL A ? 1 ? ? ? 4.664 ? 1.185 ?-0.027
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?3 Si4 ?MOL A ? 1 ? ? ? 4.900 ?-0.177 ? 1.079
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?4 ?O6 ?MOL A ? 1 ? ? ? 3.689 ?-1.438 ? 0.845
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?5 Si7 ?MOL A ? 1 ? ? ? 2.039 ?-2.056 ? 0.903
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?6 ?O8 ?MOL A ? 1 ? ? ? 2.039 ?-3.722 ? 0.332
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?7 Si9 ?MOL A ? 1 ? ? ? 1.180 ?-5.224 ? 0.014
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?8 ?O10 MOL A ? 1 ? ? ? 2.298 ?-6.420 ?-0.633
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? ?9 Si16 MOL A ? 1 ? ? ? 3.361 ?-7.028 ?-1.900
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 10 ?O17 MOL A ? 1 ? ? ? 4.535 ?-5.799 ?-2.365
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 11 Si18 MOL A ? 1 ? ? ? 5.953 ?-5.366 ?-3.320
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 12 ?O22 MOL A ? 1 ? ? ? 6.258 ?-3.639 ?-3.185
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 13 Si24 MOL A ? 1 ? ? ? 5.682 ?-1.999 ?-3.453
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 14 ?O26 MOL A ? 1 ? ? ? 6.881 ?-0.844 ?-2.890
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 15 Si28 MOL A ? 1 ? ? ? 8.517 ?-0.212 ?-3.003
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 16 ?O29 MOL A ? 1 ? ? ? 8.809 ? 0.341 ?-4.647
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 17 Si30 MOL A ? 1 ? ? ? 9.880 ? 1.056 ?-5.847
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 18 ?C34 MOL A ? 1 ? ? ? 9.732 ?-1.565 ?-2.571
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 19 ?C36 MOL A ? 1 ? ? ? 8.724 ? 1.219 ?-1.818
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 20 ?C38 MOL A ? 1 ? ? ? 6.589 ?-0.910 ? 0.760
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 21 ?C40 MOL A ? 1 ? ? ? 4.840 ? 0.411 ? 2.849
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 22 ?C42 MOL A ? 1 ? ? ? 5.390 ?-1.733 ?-5.281
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 23 ?C44 MOL A ? 1 ? ? ? 4.081 ?-1.754 ?-2.530
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 24 ?C46 MOL A ? 1 ? ? ? 7.438 ?-6.318 ?-2.702
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 25 ?C48 MOL A ? 1 ? ? ? 5.648 ?-5.792 ?-5.115
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 26 ?C50 MOL A ? 1 ? ? ? 2.341 ?-7.493 ?-3.396
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 27 ?C52 MOL A ? 1 ? ? ? 4.255 ?-8.543 ?-1.268
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 28 ?C54 MOL A ? 1 ? ? ? 0.463 ?-5.865 ? 1.617
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 29 ?C56 MOL A ? 1 ? ? ?-0.202 ?-4.925 ?-1.209
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 30 ?C58 MOL A ? 1 ? ? ? 1.433 ?-2.009 ? 2.671
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 31 ?C60 MOL A ? 1 ? ? ? 0.903 ?-1.026 ?-0.161
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 32 ?O62 MOL A ? 1 ? ? ? 3.060 ? 3.615 ? 0.318
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 33 Si63 MOL A ? 1 ? ? ? 1.891 ? 3.996 ? 1.583
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 34 ?O64 MOL A ? 1 ? ? ? 2.107 ? 5.670 ? 2.078
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 35 Si68 MOL A ? 1 ? ? ? 3.135 ? 6.928 ? 2.750
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 36 ?C69 MOL A ? 1 ? ? ? 3.667 ? 6.449 ? 4.477
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 37 ?C72 MOL A ? 1 ? ? ? 5.024 ? 3.447 ?-1.883
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 38 ?C74 MOL A ? 1 ? ? ? 2.469 ? 1.818 ?-1.953
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 39 ?C76 MOL A ? 1 ? ? ? 0.160 ? 3.770 ? 0.914
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 40 ?C78 MOL A ? 1 ? ? ? 2.129 ? 2.878 ? 3.056
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 41 ?C80 MOL A ? 1 ? ? ? 2.186 ? 8.538 ? 2.814
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 42 Si84 MOL A ? 1 ? ? ? 4.912 ? 7.172 ? 1.476
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 43 ?C84 MOL A ? 1 ? ? ? 8.985 ? 1.172 ?-7.484
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 44 ?C86 MOL A ? 1 ? ? ?10.388 ? 2.767 ?-5.292
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
ATOM ? ? 45 ?C88 MOL A ? 1 ? ? ?11.402 ?-0.013 ?-6.044
1.00 ?0.00
Post by Dallas B. Warren
Post by Yanmei Song
TER
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
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Please search the archive at http://www.gromacs.org/search
before posting!
Post by Dallas B. Warren
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--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
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--
Yanmei Song
Department of Chemical Engineering
ASU
Justin A. Lemkul
2009-04-29 22:57:07 UTC
Permalink
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)

There is probably something wrong with the .rtp entry you created. If you can
post that, perhaps someone can spot it.

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Yanmei Song
2009-04-29 23:07:08 UTC
Permalink
This is the new entry I added to the rtp file.

[ PDM ]


[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1


[ bonds ]
SI O 0.190 158805.0
SI CH3 0.164 293160.0


[ dihedrals ]
CH3 SI O SI 3.77 3 0
SI O SI CH3 3.77 3 0
O SI O SI 3.77 3 0
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you created. ?If you
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
Dallas B. Warren
2009-04-29 23:10:34 UTC
Permalink
Check consistency with other entries around it, easy way to check to see that you have the right format.

What did you edit the file with?

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O 0.190 158805.0
SI CH3 0.164 293160.0
[ dihedrals ]
CH3 SI O SI 3.77 3 0
SI O SI CH3 3.77 3 0
O SI O SI 3.77 3 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. ?If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
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Yanmei Song
2009-04-30 17:21:02 UTC
Permalink
Hi, Dallas:

I added this to the ffoplsaa.rtp

[ PDM ]

[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1

[ bonds ]
SI O
SI CH3


[ dihedrals ]
CH3 SI O SI dih_PDM_chi1_C_SI_O_SI
SI O SI CH3 dih_PDM_chi1_SI_O_SI_C
O SI O SI dih_PDM_chi1_O_SI_O_SI

The format is the same with other entries. Do you guys think anything
wrong with it?

Also what does it mean by the error message:

Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms

chain #res #atoms
1 'A' 1 45

All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp

-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289

Fatal error:
in .rtp file at line:


-------------------------------------------------------

what is "Source code file: resall.c, line: 289" It seems the problem
comes from here.

Thanks a lot!


On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
?[ atoms ]
? ? SI ? ? ?SI ? ? ? ? ? ? ?0.300 ? ? 1
? ?CH3 ? ?opls_069 ? ?0.000 ? ? 1
? ? ?O ? ? ?opls_108 ? -0.300 ? ? 1
?[ bonds ]
? ? SI ? ? O ? ? ? 0.190 ? ?158805.0
? ? SI ? CH3 ? ? 0.164 ? ?293160.0
?[ dihedrals ]
? ?CH3 ? ?SI ? ?O ? ?SI ? 3.77 ? ?3 ? ? 0
? ? SI ? ? O ? SI ? CH3 ? 3.77 ? ?3 ? ? 0
? ? ?O ? ?SI ? ?O ? ?SI ? ? 3.77 ? ?3 ? ? 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. ?If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
Justin A. Lemkul
2009-04-30 17:46:58 UTC
Permalink
Post by Yanmei Song
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O
SI CH3
[ dihedrals ]
CH3 SI O SI dih_PDM_chi1_C_SI_O_SI
SI O SI CH3 dih_PDM_chi1_SI_O_SI_C
O SI O SI dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
chain #res #atoms
1 'A' 1 45
All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" It seems the problem
comes from here.
That is the line of code that is spotting a problem.

I think the issue is that, in your original .pdb file, you have dozens of atoms
in your polymer chain, all labeled as residue 1. What your .rtp entry says is
that a single PDM should contain only three atoms. Since what you are trying to
do is make a building block, you will need to do several things:

1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue and
previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested previously,
so that termini are handled correctly (since the -n.tdb and -c.tdb files cannot
be used for non-protein).

See the amino acid entries for examples on how to use + and - appropriately, or
the list archive for examples provided by other users for other polymers
(polyethylene is especially common), for example:

http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html

-Justin
Post by Yanmei Song
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O 0.190 158805.0
SI CH3 0.164 293160.0
[ dihedrals ]
CH3 SI O SI 3.77 3 0
SI O SI CH3 3.77 3 0
O SI O SI 3.77 3 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Yanmei Song
2009-04-30 18:06:50 UTC
Permalink
Hi, Justin:

Thank you so much for your nice help. I will work on that according to
your suggestions.
Post by Justin A. Lemkul
Post by Yanmei Song
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
? ? ?SI ? ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ? 1
? CH3 ? ? ?opls_069 ? ?0.000 ? ? 1
? ? ? O ? ? ? opls_108 ? -0.300 ? ? 1
?[ bonds ]
? ?SI ? ? O
? ?SI ? CH3
?[ dihedrals ]
? CH3 ? ?SI ? ?O ? ? ?SI ? ? dih_PDM_chi1_C_SI_O_SI
? ? ?SI ? ? O ? SI ? CH3 ? ? dih_PDM_chi1_SI_O_SI_C
? ? ? O ? ?SI ? ?O ? ? ?SI ? ? ?dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
?chain ?#res #atoms
?1 'A' ? ? 1 ? ? 45
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" ?It seems the problem
comes from here.
That is the line of code that is spotting a problem.
I think the issue is that, in your original .pdb file, you have dozens of
atoms in your polymer chain, all labeled as residue 1. ?What your .rtp entry
says is that a single PDM should contain only three atoms. ?Since what you
are trying to do is make a building block, you will need to do several
1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue
and previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested
previously, so that termini are handled correctly (since the -n.tdb and
-c.tdb files cannot be used for non-protein).
See the amino acid entries for examples on how to use + and - appropriately,
or the list archive for examples provided by other users for other polymers
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
-Justin
Post by Yanmei Song
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see
that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
?[ atoms ]
? ?SI ? ? ?SI ? ? ? ? ? ? ?0.300 ? ? 1
? CH3 ? ?opls_069 ? ?0.000 ? ? 1
? ? O ? ? ?opls_108 ? -0.300 ? ? 1
?[ bonds ]
? ?SI ? ? O ? ? ? 0.190 ? ?158805.0
? ?SI ? CH3 ? ? 0.164 ? ?293160.0
?[ dihedrals ]
? CH3 ? ?SI ? ?O ? ?SI ? 3.77 ? ?3 ? ? 0
? ?SI ? ? O ? SI ? CH3 ? 3.77 ? ?3 ? ? 0
? ? O ? ?SI ? ?O ? ?SI ? ? 3.77 ? ?3 ? ? 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. ?If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
ROHIT MALSHE
2009-04-30 18:40:58 UTC
Permalink
Hi all,

I want to simulate a molecule which has many benzene rings attached to each other. However I want to coarsegrain the system a lot !!

I want to represent the center of masses of benzene rings with point masses. For all the parameters, such as bonds, angles, dihedrals I can use similar parameters as these are very rigid molecules but I am confused what Lennard Jones parameters should I use for these super atoms !

Can someone suggest how I can iteratively do that starting from a first guess ?

Any suggestions are most welcome !


__________________________________________________________________________________________________________
Rohit Malshe 1112, Engineering Hall Tel :001 608 262 3370
Graduate Student 1415, Engineering Drive Email: malshe at wisc.edu
Chemical and Biological Engineering Madison, WI.
University of Wisconsin-Madison USA USA- 53726
__________________________________________________________________________________________________________
Justin A. Lemkul
2009-04-30 18:48:09 UTC
Permalink
Post by ROHIT MALSHE
Hi all,
I want to simulate a molecule which has many benzene rings attached to each
other. However I want to coarsegrain the system a lot !!
I want to represent the center of masses of benzene rings with point masses.
For all the parameters, such as bonds, angles, dihedrals I can use similar
parameters as these are very rigid molecules but I am confused what Lennard
Jones parameters should I use for these super atoms !
Can someone suggest how I can iteratively do that starting from a first guess ?
The best advice for developing parameters (for any type of system) is to read
relevant literature, decide on a derivation scheme, and set to work. There is
no substitute for doing your own homework!

-Justin
Post by ROHIT MALSHE
Any suggestions are most welcome !
__________________________________________________________________________________________________________
Rohit Malshe 1112,
Engineering Hall Tel :001 608 262 3370
Graduate Student 1415,
Engineering Drive Email: malshe at wisc.edu Chemical and Biological
Engineering Madison, WI. University of Wisconsin-Madison USA
USA- 53726
__________________________________________________________________________________________________________
_______________________________________________ gmx-users mailing list
gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org. Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Xavier Periole
2009-05-01 07:16:18 UTC
Permalink
On Thu, 30 Apr 2009 13:40:58 -0500
Post by ROHIT MALSHE
Hi all,
I want to simulate a molecule which has many benzene rings attached to each
other. However I want to coarsegrain the system a lot !!
Did you look at the Martini CG force field. It should be help full.
You can google it.
Post by ROHIT MALSHE
I want to represent the center of masses of benzene rings with point masses.
For all the parameters, such as bonds, angles, dihedrals I can use similar
parameters as these are very rigid molecules but I am confused what Lennard
Jones parameters should I use for these super atoms !
Can someone suggest how I can iteratively do that starting from a first guess ?
Any suggestions are most welcome !
__________________________________________________________________________________________________________
Rohit Malshe 1112,
Engineering Hall Tel :001 608 262 3370
Graduate Student 1415,
Engineering Drive Email: malshe at wisc.edu
Chemical and Biological Engineering Madison, WI.
University of Wisconsin-Madison USA USA- 53726
__________________________________________________________________________________________________________
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------
Yanmei Song
2009-04-30 20:29:01 UTC
Permalink
Sorry to bother so many times.

I edited the rtp and added the new residue as following, which I think
should be no problem.

[ PDM ]

[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1

[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1


; Terminal PDMS residue ("beginning" of chain)

[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1

[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1


; Terminal PDMS residue ("end" of chain)


[ PDME ]
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1

[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3

Also my pdb is :

ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
TER

after pdb2gmx, I still got the error:

Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms

chain #res #atoms
1 ' ' 3 13

All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp

-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289

Fatal error:
in .rtp file at line:


-------------------------------------------------------

Anyone knows where I did wrong?

Thank you so much!
Post by Justin A. Lemkul
Post by Yanmei Song
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
? ? ?SI ? ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ? 1
? CH3 ? ? ?opls_069 ? ?0.000 ? ? 1
? ? ? O ? ? ? opls_108 ? -0.300 ? ? 1
?[ bonds ]
? ?SI ? ? O
? ?SI ? CH3
?[ dihedrals ]
? CH3 ? ?SI ? ?O ? ? ?SI ? ? dih_PDM_chi1_C_SI_O_SI
? ? ?SI ? ? O ? SI ? CH3 ? ? dih_PDM_chi1_SI_O_SI_C
? ? ? O ? ?SI ? ?O ? ? ?SI ? ? ?dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
?chain ?#res #atoms
?1 'A' ? ? 1 ? ? 45
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" ?It seems the problem
comes from here.
That is the line of code that is spotting a problem.
I think the issue is that, in your original .pdb file, you have dozens of
atoms in your polymer chain, all labeled as residue 1. ?What your .rtp entry
says is that a single PDM should contain only three atoms. ?Since what you
are trying to do is make a building block, you will need to do several
1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue
and previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested
previously, so that termini are handled correctly (since the -n.tdb and
-c.tdb files cannot be used for non-protein).
See the amino acid entries for examples on how to use + and - appropriately,
or the list archive for examples provided by other users for other polymers
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
-Justin
Post by Yanmei Song
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see
that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
?[ atoms ]
? ?SI ? ? ?SI ? ? ? ? ? ? ?0.300 ? ? 1
? CH3 ? ?opls_069 ? ?0.000 ? ? 1
? ? O ? ? ?opls_108 ? -0.300 ? ? 1
?[ bonds ]
? ?SI ? ? O ? ? ? 0.190 ? ?158805.0
? ?SI ? CH3 ? ? 0.164 ? ?293160.0
?[ dihedrals ]
? CH3 ? ?SI ? ?O ? ?SI ? 3.77 ? ?3 ? ? 0
? ?SI ? ? O ? SI ? CH3 ? 3.77 ? ?3 ? ? 0
? ? O ? ?SI ? ?O ? ?SI ? ? 3.77 ? ?3 ? ? 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. ?If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
Justin A. Lemkul
2009-05-01 00:04:04 UTC
Permalink
Your system works for me under Gromacs 4.0.4 - the only issue is that your PDME
residue has a net +0.3 charge. Does your Gromacs installation work properly for
proven systems like proteins?

I would suggest upgrading to version 4.0.4 and trying again. If that does not
work, post to the list a complete description of your hardware and software -
OS, version, compilers used, configuration options, etc, and see if anyone can
spot a problem.

-Justin
Post by Yanmei Song
Sorry to bother so many times.
I edited the rtp and added the new residue as following, which I think
should be no problem.
[ PDM ]
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PDMS residue ("end" of chain)
[ PDME ]
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
TER
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Anyone knows where I did wrong?
Thank you so much!
Post by Justin A. Lemkul
Post by Yanmei Song
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O
SI CH3
[ dihedrals ]
CH3 SI O SI dih_PDM_chi1_C_SI_O_SI
SI O SI CH3 dih_PDM_chi1_SI_O_SI_C
O SI O SI dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
chain #res #atoms
1 'A' 1 45
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" It seems the problem
comes from here.
That is the line of code that is spotting a problem.
I think the issue is that, in your original .pdb file, you have dozens of
atoms in your polymer chain, all labeled as residue 1. What your .rtp entry
says is that a single PDM should contain only three atoms. Since what you
are trying to do is make a building block, you will need to do several
1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue
and previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested
previously, so that termini are handled correctly (since the -n.tdb and
-c.tdb files cannot be used for non-protein).
See the amino acid entries for examples on how to use + and - appropriately,
or the list archive for examples provided by other users for other polymers
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
-Justin
Post by Yanmei Song
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see
that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O 0.190 158805.0
SI CH3 0.164 293160.0
[ dihedrals ]
CH3 SI O SI 3.77 3 0
SI O SI CH3 3.77 3 0
O SI O SI 3.77 3 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Yanmei Song
2009-05-01 00:11:08 UTC
Permalink
That means both the rtp and pdb files work in your GROMACS-4.0.4. For
the issue of" PDME residue has a net +0.3 charge" , I should change
the charge to 0 for Si in PDME, which I have ignored. I will update
the software and see if it works. Thanks so much for your help!
Post by Justin A. Lemkul
Your system works for me under Gromacs 4.0.4 - the only issue is that your
PDME residue has a net +0.3 charge. ?Does your Gromacs installation work
properly for proven systems like proteins?
I would suggest upgrading to version 4.0.4 and trying again. ?If that does
not work, post to the list a complete description of your hardware and
software - OS, version, compilers used, configuration options, etc, and see
if anyone can spot a problem.
-Justin
Post by Yanmei Song
Sorry to bother so many times.
I edited the rtp and added the new residue as following, which I think
should be no problem.
[ PDM ]
?[ atoms ]
? ?SI1 ? ?SI ? ? ? ? ? ? ? ? 0.300 ? ?1
? ? C1 ? opls_069 ? ? 0.000 ? ?1
? ? C2 ? opls_069 ? ? 0.000 ? ?1
? ? O1 ? opls_108 ? ?-0.300 ? ?1
?[ bonds ]
? ?SI1 ? -O1
? ?SI1 ? ?C1
? ?SI1 ? ?C2
? ?SI1 ? ?O1
? ?O1 ? +SI1
; Terminal ?PDMS residue ("beginning" of chain)
[ PDMB ]
?[ atoms ]
? ?C1 ? ?opls_069 ? ? 0.000 ? ?1
? SI1 ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ?1
? ?C2 ? ?opls_069 ? ? 0.000 ? ?1
? ?C3 ? ?opls_069 ? ? 0.000 ? ?1
? ?O1 ? ?opls_108 ? ?-0.300 ? ?1
?[ bonds ]
? ?SI1 ? C1
? ?SI1 ? C2
? ?SI1 ? C3
? ?SI1 ? O1
? ? O1 ? +SI1
; Terminal PDMS residue ("end" of chain)
[ PDME ]
?[ atoms ]
? SI1 ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ?1
? ?C1 ? ?opls_069 ? ? 0.000 ? ?1
? ?C2 ? ?opls_069 ? ? 0.000 ? ?1
? ?C3 ? ?opls_069 ? ? 0.000 ? ?1
?[ bonds ]
? ?SI1 ? -O1
? ?SI1 ? C1
? ?SI1 ? C2
? ?SI1 ? C3
ATOM ? ? ?1 SI1 ?PDMB ? ?1 ? ? ? 8.995 ?-3.779 ?-2.091 ?1.00 ?0.00
ATOM ? ? ?2 ?C1 ?PDMB ? ?1 ? ? ?10.682 ?-3.453 ?-2.828 ?1.00 ?0.00
ATOM ? ? ?3 ?C2 ?PDMB ? ?1 ? ? ? 8.020 ?-2.184 ?-2.039 ?1.00 ?0.00
ATOM ? ? ?4 ?O1 ?PDMB ? ?1 ? ? ? 8.142 ?-4.958 ?-3.082 ?1.00 ?0.00
ATOM ? ? ?5 ?C3 ?PDMB ? ?1 ? ? ? 9.192 ?-4.446 ?-0.356 ?1.00 ?0.00
ATOM ? ? ?6 SI1 ?PDM ? ? 2 ? ? ? 6.710 ?-5.932 ?-3.395 ?1.00 ?0.00
ATOM ? ? ?7 ?O1 ?PDM ? ? 2 ? ? ? 6.960 ?-6.886 ?-4.852 ?1.00 ?0.00
ATOM ? ? ?8 ?C1 ?PDM ? ? 2 ? ? ? 6.403 ?-7.074 ?-1.946 ?1.00 ?0.00
ATOM ? ? ?9 ?C2 ?PDM ? ? 2 ? ? ? 5.231 ?-4.812 ?-3.628 ?1.00 ?0.00
ATOM ? ? 10 SI1 ?PDME ? ?3 ? ? ? 6.370 ?-8.062 ?-6.022 ?1.00 ?0.00
ATOM ? ? 11 ?C1 ?PDME ? ?3 ? ? ? 7.679 ?-8.351 ?-7.325 ?1.00 ?0.00
ATOM ? ? 12 ?C2 ?PDME ? ?3 ? ? ? 5.990 ?-9.673 ?-5.153 ?1.00 ?0.00
ATOM ? ? 13 ?C3 ?PDME ? ?3 ? ? ? 4.816 ?-7.411 ?-6.834 ?1.00 ?0.00
TER
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
?chain ?#res #atoms
?1 ' ' ? ? 3 ? ? 13
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Anyone knows where I did wrong?
Thank you so much!
Post by Justin A. Lemkul
Post by Yanmei Song
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
? ? SI ? ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ? 1
?CH3 ? ? ?opls_069 ? ?0.000 ? ? 1
? ? ?O ? ? ? opls_108 ? -0.300 ? ? 1
?[ bonds ]
? SI ? ? O
? SI ? CH3
?[ dihedrals ]
?CH3 ? ?SI ? ?O ? ? ?SI ? ? dih_PDM_chi1_C_SI_O_SI
? ? SI ? ? O ? SI ? CH3 ? ? dih_PDM_chi1_SI_O_SI_C
? ? ?O ? ?SI ? ?O ? ? ?SI ? ? ?dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
?chain ?#res #atoms
?1 'A' ? ? 1 ? ? 45
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" ?It seems the problem
comes from here.
That is the line of code that is spotting a problem.
I think the issue is that, in your original .pdb file, you have dozens of
atoms in your polymer chain, all labeled as residue 1. ?What your .rtp entry
says is that a single PDM should contain only three atoms. ?Since what you
are trying to do is make a building block, you will need to do several
1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue
and previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested
previously, so that termini are handled correctly (since the -n.tdb and
-c.tdb files cannot be used for non-protein).
See the amino acid entries for examples on how to use + and - appropriately,
or the list archive for examples provided by other users for other polymers
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
-Justin
Post by Yanmei Song
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see
that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble
a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
?[ atoms ]
? SI ? ? ?SI ? ? ? ? ? ? ?0.300 ? ? 1
?CH3 ? ?opls_069 ? ?0.000 ? ? 1
? ?O ? ? ?opls_108 ? -0.300 ? ? 1
?[ bonds ]
? SI ? ? O ? ? ? 0.190 ? ?158805.0
? SI ? CH3 ? ? 0.164 ? ?293160.0
?[ dihedrals ]
?CH3 ? ?SI ? ?O ? ?SI ? 3.77 ? ?3 ? ? 0
? SI ? ? O ? SI ? CH3 ? 3.77 ? ?3 ? ? 0
? ?O ? ?SI ? ?O ? ?SI ? ? 3.77 ? ?3 ? ? 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. ?If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
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Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
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--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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--
Yanmei Song
Department of Chemical Engineering
ASU
Yanmei Song
2009-05-04 23:47:02 UTC
Permalink
Dear Justin:

Thank you so much for your help earlier. I updated my GROMACS to
4.0.4. When I run pdb2gmx using the following two files. I still got
the similar error message:

Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms

chain #res #atoms
1 ' ' 3 13

All occupancies are one
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp

-------------------------------------------------------
Program pdb2gmx_d, VERSION 4.0.4
Source code file: resall.c, line: 279

Fatal error:
in .rtp file at line:


-------------------------------------------------------

My new residue added to ffoplass.rtp is:
[ PDM ]
; designation arbitrary, C1 and C2 is -CH3
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1

[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1


; Terminal PDMS residue ("beginning" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1

[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1


; Terminal PE residue ("end" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3

[ PDME ]
[ atoms ]
SI1 SI 0.000 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1

[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3

PDB file:

ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
TER

Thanks a lot!
Post by Justin A. Lemkul
Your system works for me under Gromacs 4.0.4 - the only issue is that your
PDME residue has a net +0.3 charge. ?Does your Gromacs installation work
properly for proven systems like proteins?
I would suggest upgrading to version 4.0.4 and trying again. ?If that does
not work, post to the list a complete description of your hardware and
software - OS, version, compilers used, configuration options, etc, and see
if anyone can spot a problem.
-Justin
Post by Yanmei Song
Sorry to bother so many times.
I edited the rtp and added the new residue as following, which I think
should be no problem.
[ PDM ]
?[ atoms ]
? ?SI1 ? ?SI ? ? ? ? ? ? ? ? 0.300 ? ?1
? ? C1 ? opls_069 ? ? 0.000 ? ?1
? ? C2 ? opls_069 ? ? 0.000 ? ?1
? ? O1 ? opls_108 ? ?-0.300 ? ?1
?[ bonds ]
? ?SI1 ? -O1
? ?SI1 ? ?C1
? ?SI1 ? ?C2
? ?SI1 ? ?O1
? ?O1 ? +SI1
; Terminal ?PDMS residue ("beginning" of chain)
[ PDMB ]
?[ atoms ]
? ?C1 ? ?opls_069 ? ? 0.000 ? ?1
? SI1 ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ?1
? ?C2 ? ?opls_069 ? ? 0.000 ? ?1
? ?C3 ? ?opls_069 ? ? 0.000 ? ?1
? ?O1 ? ?opls_108 ? ?-0.300 ? ?1
?[ bonds ]
? ?SI1 ? C1
? ?SI1 ? C2
? ?SI1 ? C3
? ?SI1 ? O1
? ? O1 ? +SI1
; Terminal PDMS residue ("end" of chain)
[ PDME ]
?[ atoms ]
? SI1 ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ?1
? ?C1 ? ?opls_069 ? ? 0.000 ? ?1
? ?C2 ? ?opls_069 ? ? 0.000 ? ?1
? ?C3 ? ?opls_069 ? ? 0.000 ? ?1
?[ bonds ]
? ?SI1 ? -O1
? ?SI1 ? C1
? ?SI1 ? C2
? ?SI1 ? C3
ATOM ? ? ?1 SI1 ?PDMB ? ?1 ? ? ? 8.995 ?-3.779 ?-2.091 ?1.00 ?0.00
ATOM ? ? ?2 ?C1 ?PDMB ? ?1 ? ? ?10.682 ?-3.453 ?-2.828 ?1.00 ?0.00
ATOM ? ? ?3 ?C2 ?PDMB ? ?1 ? ? ? 8.020 ?-2.184 ?-2.039 ?1.00 ?0.00
ATOM ? ? ?4 ?O1 ?PDMB ? ?1 ? ? ? 8.142 ?-4.958 ?-3.082 ?1.00 ?0.00
ATOM ? ? ?5 ?C3 ?PDMB ? ?1 ? ? ? 9.192 ?-4.446 ?-0.356 ?1.00 ?0.00
ATOM ? ? ?6 SI1 ?PDM ? ? 2 ? ? ? 6.710 ?-5.932 ?-3.395 ?1.00 ?0.00
ATOM ? ? ?7 ?O1 ?PDM ? ? 2 ? ? ? 6.960 ?-6.886 ?-4.852 ?1.00 ?0.00
ATOM ? ? ?8 ?C1 ?PDM ? ? 2 ? ? ? 6.403 ?-7.074 ?-1.946 ?1.00 ?0.00
ATOM ? ? ?9 ?C2 ?PDM ? ? 2 ? ? ? 5.231 ?-4.812 ?-3.628 ?1.00 ?0.00
ATOM ? ? 10 SI1 ?PDME ? ?3 ? ? ? 6.370 ?-8.062 ?-6.022 ?1.00 ?0.00
ATOM ? ? 11 ?C1 ?PDME ? ?3 ? ? ? 7.679 ?-8.351 ?-7.325 ?1.00 ?0.00
ATOM ? ? 12 ?C2 ?PDME ? ?3 ? ? ? 5.990 ?-9.673 ?-5.153 ?1.00 ?0.00
ATOM ? ? 13 ?C3 ?PDME ? ?3 ? ? ? 4.816 ?-7.411 ?-6.834 ?1.00 ?0.00
TER
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
?chain ?#res #atoms
?1 ' ' ? ? 3 ? ? 13
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Anyone knows where I did wrong?
Thank you so much!
Post by Justin A. Lemkul
Post by Yanmei Song
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
? ? SI ? ? ? SI ? ? ? ? ? ? ? ? 0.300 ? ? 1
?CH3 ? ? ?opls_069 ? ?0.000 ? ? 1
? ? ?O ? ? ? opls_108 ? -0.300 ? ? 1
?[ bonds ]
? SI ? ? O
? SI ? CH3
?[ dihedrals ]
?CH3 ? ?SI ? ?O ? ? ?SI ? ? dih_PDM_chi1_C_SI_O_SI
? ? SI ? ? O ? SI ? CH3 ? ? dih_PDM_chi1_SI_O_SI_C
? ? ?O ? ?SI ? ?O ? ? ?SI ? ? ?dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
?chain ?#res #atoms
?1 'A' ? ? 1 ? ? 45
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" ?It seems the problem
comes from here.
That is the line of code that is spotting a problem.
I think the issue is that, in your original .pdb file, you have dozens of
atoms in your polymer chain, all labeled as residue 1. ?What your .rtp entry
says is that a single PDM should contain only three atoms. ?Since what you
are trying to do is make a building block, you will need to do several
1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue
and previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested
previously, so that termini are handled correctly (since the -n.tdb and
-c.tdb files cannot be used for non-protein).
See the amino acid entries for examples on how to use + and - appropriately,
or the list archive for examples provided by other users for other polymers
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
-Justin
Post by Yanmei Song
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see
that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble
a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
?[ atoms ]
? SI ? ? ?SI ? ? ? ? ? ? ?0.300 ? ? 1
?CH3 ? ?opls_069 ? ?0.000 ? ? 1
? ?O ? ? ?opls_108 ? -0.300 ? ? 1
?[ bonds ]
? SI ? ? O ? ? ? 0.190 ? ?158805.0
? SI ? CH3 ? ? 0.164 ? ?293160.0
?[ dihedrals ]
?CH3 ? ?SI ? ?O ? ?SI ? 3.77 ? ?3 ? ? 0
? SI ? ? O ? SI ? CH3 ? 3.77 ? ?3 ? ? 0
? ?O ? ?SI ? ?O ? ?SI ? ? 3.77 ? ?3 ? ? 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. ?If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list ? ?gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Yanmei Song
Department of Chemical Engineering
ASU
Justin A. Lemkul
2009-05-04 23:53:53 UTC
Permalink
Then it seems clear to me that your installation of Gromacs is faulty. Have you
tried running the test set (available on the wiki site)? If you can describe
your computer system (OS, version, compilers used, configuration options, etc.)
then perhaps someone on the list can spot a potential pitfall.

-Justin
Post by Yanmei Song
Thank you so much for your help earlier. I updated my GROMACS to
4.0.4. When I run pdb2gmx using the following two files. I still got
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx_d, VERSION 4.0.4
Source code file: resall.c, line: 279
-------------------------------------------------------
[ PDM ]
; designation arbitrary, C1 and C2 is -CH3
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PE residue ("end" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDME ]
[ atoms ]
SI1 SI 0.000 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
TER
Thanks a lot!
Post by Justin A. Lemkul
Your system works for me under Gromacs 4.0.4 - the only issue is that your
PDME residue has a net +0.3 charge. Does your Gromacs installation work
properly for proven systems like proteins?
I would suggest upgrading to version 4.0.4 and trying again. If that does
not work, post to the list a complete description of your hardware and
software - OS, version, compilers used, configuration options, etc, and see
if anyone can spot a problem.
-Justin
Post by Yanmei Song
Sorry to bother so many times.
I edited the rtp and added the new residue as following, which I think
should be no problem.
[ PDM ]
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PDMS residue ("end" of chain)
[ PDME ]
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
TER
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Anyone knows where I did wrong?
Thank you so much!
Post by Justin A. Lemkul
Post by Yanmei Song
I added this to the ffoplsaa.rtp
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O
SI CH3
[ dihedrals ]
CH3 SI O SI dih_PDM_chi1_C_SI_O_SI
SI O SI CH3 dih_PDM_chi1_SI_O_SI_C
O SI O SI dih_PDM_chi1_O_SI_O_SI
The format is the same with other entries. Do you guys think anything
wrong with it?
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
chain #res #atoms
1 'A' 1 45
All occupancies are one
Opening library file
/packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
what is "Source code file: resall.c, line: 289" It seems the problem
comes from here.
That is the line of code that is spotting a problem.
I think the issue is that, in your original .pdb file, you have dozens of
atoms in your polymer chain, all labeled as residue 1. What your .rtp entry
says is that a single PDM should contain only three atoms. Since what you
are trying to do is make a building block, you will need to do several
1. Re-number your .pdb file so that multiple monomers are apparent.
2. Use the + and - characters to indicate connectivity to the next residue
and previous residue, respectively.
3. Create separate .rtp entries for terminal groups, as I suggested
previously, so that termini are handled correctly (since the -n.tdb and
-c.tdb files cannot be used for non-protein).
See the amino acid entries for examples on how to use + and - appropriately,
or the list archive for examples provided by other users for other polymers
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
-Justin
Post by Yanmei Song
Thanks a lot!
On Wed, Apr 29, 2009 at 4:10 PM, Dallas B. Warren
Post by Dallas B. Warren
Check consistency with other entries around it, easy way to check to see
that you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble
a nail.
-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yanmei Song
Sent: Thursday, 30 April 2009 9:07 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Error by pdb2gmx
This is the new entry I added to the rtp file.
[ PDM ]
[ atoms ]
SI SI 0.300 1
CH3 opls_069 0.000 1
O opls_108 -0.300 1
[ bonds ]
SI O 0.190 158805.0
SI CH3 0.164 293160.0
[ dihedrals ]
CH3 SI O SI 3.77 3 0
SI O SI CH3 3.77 3 0
O SI O SI 3.77 3 0
On Wed, Apr 29, 2009 at 3:57 PM, Justin A. Lemkul
Post by Justin A. Lemkul
Post by Yanmei Song
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
-------------------------------------------------------
Well that's not a terribly helpful error message, is it? :)
There is probably something wrong with the .rtp entry you
created. If you
Post by Justin A. Lemkul
can post that, perhaps someone can spot it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Post by Justin A. Lemkul
Please don't post (un)subscribe requests to the list. Use
the www interface
Post by Justin A. Lemkul
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
Mark Abraham
2009-05-05 05:15:28 UTC
Permalink
Post by Justin A. Lemkul
Then it seems clear to me that your installation of Gromacs is faulty.
Have you tried running the test set (available on the wiki site)? If
you can describe your computer system (OS, version, compilers used,
configuration options, etc.) then perhaps someone on the list can spot a
potential pitfall.
-Justin
Post by Yanmei Song
Thank you so much for your help earlier. I updated my GROMACS to
4.0.4. When I run pdb2gmx using the following two files. I still got
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading pdms2.pdb...
Read 13 atoms
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx_d, VERSION 4.0.4
Source code file: resall.c, line: 279
-------------------------------------------------------
This error is being provoked at the top of the .rtp file when a line
with something like "[header]" is not parsing suitably. A while ago I
suggested using diff on the .rtp file. Do that.

Mark
Yanmei Song
2009-05-05 16:27:53 UTC
Permalink
Dear Mark:

This error is being provoked at the top of the .rtp file when a line with
something like "[header]" is not parsing suitably. A while ago I suggested
using diff on the .rtp file. Do that.


Would you mind telling me how to do that in detail?

I tried the following and it doesn't work.

diff
[ PDM ]
; designation arbitrary, C1 and C2 is -CH3
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1

[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1


; Terminal PDMS residue ("beginning" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1

[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1


; Terminal PE residue ("end" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3

[ PDME ]
[ atoms ]
SI1 SI 0.000 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1

[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
diff



Thanks a lot in advance!


On Mon, May 4, 2009 at 10:15 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
Post by Justin A. Lemkul
Then it seems clear to me that your installation of Gromacs is faulty.
Have you tried running the test set (available on the wiki site)? If
you
Post by Justin A. Lemkul
can describe your computer system (OS, version, compilers used,
configuration options, etc.) then perhaps someone on the list can spot a
potential pitfall.
-Justin
Post by Yanmei Song
Thank you so much for your help earlier. I updated my GROMACS to
4.0.4. When I run pdb2gmx using the following two files. I still got
Opening library file ffoplsaa.rtp
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
Post by Justin A. Lemkul
Post by Yanmei Song
Entries in dgsolv.dat: 7
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading pdms2.pdb...
Read 13 atoms
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file
/packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx_d, VERSION 4.0.4
Source code file: resall.c, line: 279
-------------------------------------------------------
This error is being provoked at the top of the .rtp file when a line with
something like "[header]" is not parsing suitably. A while ago I suggested
using diff on the .rtp file. Do that.
Mark
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Yanmei Song
Department of Chemical Engineering
ASU
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Mark Abraham
2009-05-05 16:35:52 UTC
Permalink
Post by Yanmei Song
This error is being provoked at the top of the .rtp file when a line with
something like "[header]" is not parsing suitably. A while ago I suggested
using diff on the .rtp file. Do that.
Would you mind telling me how to do that in detail?
On a command line, "diff oldfile newfile". Try Googling and reading the
man page for diff.

Mark

Mark Abraham
2009-04-29 22:54:07 UTC
Permalink
Post by Yanmei Song
Thank you for your help earlier.
I made a copy of ffoplsaa.rtp to my working directory and add a new
pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat
0: GROMOS96 43a1 force field
1: GROMOS96 43b1 vacuum force field
2: GROMOS96 43a2 force field (improved alkane dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: Encad all-atom force field, using scaled-down vacuum charges
8: Encad all-atom force field, using full solvent charges
6
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
chain #res #atoms
1 'A' 1 45
All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
Well that's weird. You should use the "diff" utility on ffoplsaa.rtp
before and after your modifications and see what that tells you.

If you've edited it on a Windows machine, then you may have line-ending
issues. If so, use "dos2unix" on the file.

Mark
wuxiao
2009-05-05 03:53:42 UTC
Permalink
Dear Song,

I guess that the problem you encountered does not matter the GROMACS. On contrary, I think that you must have edited the pdb file and made mistakes of the file format so that pdb2gmx can not tell it correctly. I wish this information can help you to deal with the problem.



xiaowu
Post by Yanmei Song
Thank you so much for your help earlier. I updated my GROMACS to
4.0.4. When I run pdb2gmx using the following two files. I still got
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading pdms2.pdb...
Read 13 atoms
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 13 atoms
chain #res #atoms
1 ' ' 3 13
All occupancies are one
Opening library file /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
Atomtype 1
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx_d, VERSION 4.0.4
Source code file: resall.c, line: 279
-------------------------------------------------------
[ PDM ]
; designation arbitrary, C1 and C2 is -CH3
[ atoms ]
SI1 SI 0.300 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 O1
O1 +SI1
; Terminal PDMS residue ("beginning" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDMB ]
[ atoms ]
C1 opls_069 0.000 1
SI1 SI 0.300 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
O1 opls_108 -0.300 1
[ bonds ]
SI1 C1
SI1 C2
SI1 C3
SI1 O1
O1 +SI1
; Terminal PE residue ("end" of chain)
; designation arbitrary, C1 C2 and C3 is -CH3
[ PDME ]
[ atoms ]
SI1 SI 0.000 1
C1 opls_069 0.000 1
C2 opls_069 0.000 1
C3 opls_069 0.000 1
[ bonds ]
SI1 -O1
SI1 C1
SI1 C2
SI1 C3
ATOM 1 SI1 PDMB 1 8.995 -3.779 -2.091 1.00 0.00
ATOM 2 C1 PDMB 1 10.682 -3.453 -2.828 1.00 0.00
ATOM 3 C2 PDMB 1 8.020 -2.184 -2.039 1.00 0.00
ATOM 4 O1 PDMB 1 8.142 -4.958 -3.082 1.00 0.00
ATOM 5 C3 PDMB 1 9.192 -4.446 -0.356 1.00 0.00
ATOM 6 SI1 PDM 2 6.710 -5.932 -3.395 1.00 0.00
ATOM 7 O1 PDM 2 6.960 -6.886 -4.852 1.00 0.00
ATOM 8 C1 PDM 2 6.403 -7.074 -1.946 1.00 0.00
ATOM 9 C2 PDM 2 5.231 -4.812 -3.628 1.00 0.00
ATOM 10 SI1 PDME 3 6.370 -8.062 -6.022 1.00 0.00
ATOM 11 C1 PDME 3 7.679 -8.351 -7.325 1.00 0.00
ATOM 12 C2 PDME 3 5.990 -9.673 -5.153 1.00 0.00
ATOM 13 C3 PDME 3 4.816 -7.411 -6.834 1.00 0.00
TER
Thanks a lot!
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