Discussion:
methanol as a solvent
(too old to reply)
Alok
2004-09-29 08:15:26 UTC
Permalink
Hello,

i was trying to solvate speptide(given in tutotorial of gromacs)
by methanol in place of SPC .
i did first two steps same as given in tutorial for speptide
(pdb2gmx,editconf).
For genbox i only change the solvent input file. i specified
meoh_WFG.gro in place of spc216.gro (which is uploaded by "Christoph
Freudenberger" in gromacs topogies. thanks for it )

genbox -cp out -cs meoh_WFG.gro -p speptide -o b4em

my problem is that solvent(methanol) is not added in speptide.top file.
can someone point out my mistake.
Thanks in advance.

i am attaching the output of genbox :-

Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/share/gromacs/top/atommass.dat
Opening library file /usr/local/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
Go Rough, Oppose Many Angry Chinese Serial killers
Containing 191 atoms in 19 residues
Initialising van der waals distances...
Reading solvent configuration
"MeOH solvent box, 400 molecules, CF 13/03/03"
solvent configuration contains 1200 atoms in 400 residues

Initialising van der waals distances...
Will generate new solvent configuration of 1x2x1 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
MeOH ( 3 atoms): 800 residues
Calculating Overlap...
box_margin = 0.315
Removed 609 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
Generated table with 0 data points for COUL.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 2591 charge groups and 2591 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 12 x 19 x 10 cells
Succesfully made neighbourlist
nri = 4450, nrj = 50057
Checking Protein-Solvent overlap: tested 1864 pairs, removed 162 atoms.
Checking Solvent-Solvent overlap: tested 11554 pairs, removed 255 atoms.
Added 458 molecules
Generated solvent containing 1374 atoms in 458 residues
Writing generated configuration to b4em.gro
Go Rough, Oppose Many Angry Chinese Serial killers

Output configuration contains 1565 atoms in 477 residues
Volume : 34.9038 (nm^3)
Density : 731.971 (g/l)
Number of SOL molecules: 0



Alok jain
Indian Institute of Tecnology
Kanpur, India
Nuno R. L. Ferreira
2004-09-29 08:31:35 UTC
Permalink
Hi Alok

IIRC, now you just have to edit your topology file by hand.
Right under the #include describing the peptide, put the .itp of methanol.

Like for e.g.:

; Include forcefield parameters
#include "ffG43a1.itp"
#include "meoh_wfg.itp" ; check the .itp name

and at the tail of your .top file, add one line with specifying the number
of methanol molecules added to the system.

Methanol 458 ; check the name of [ moleculetype ] under .itp
And you're done.

Best regards.
Nuno


----- Original Message -----
From: "Alok" <alokjain at iitk.ac.in>
To: <gmx-users at gromacs.org>
Sent: Wednesday, September 29, 2004 9:15 AM
Subject: [gmx-users] methanol as a solvent


Hello,

i was trying to solvate speptide(given in tutotorial of gromacs)
by methanol in place of SPC .
i did first two steps same as given in tutorial for speptide
(pdb2gmx,editconf).
For genbox i only change the solvent input file. i specified
meoh_WFG.gro in place of spc216.gro (which is uploaded by "Christoph
Freudenberger" in gromacs topogies. thanks for it )

genbox -cp out -cs meoh_WFG.gro -p speptide -o b4em

my problem is that solvent(methanol) is not added in speptide.top file.
can someone point out my mistake.
Thanks in advance.

i am attaching the output of genbox :-

Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Opening library file /usr/local/share/gromacs/top/atommass.dat
Opening library file /usr/local/share/gromacs/top/vdwradii.dat
Opening library file /usr/local/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading solute configuration
Go Rough, Oppose Many Angry Chinese Serial killers
Containing 191 atoms in 19 residues
Initialising van der waals distances...
Reading solvent configuration
"MeOH solvent box, 400 molecules, CF 13/03/03"
solvent configuration contains 1200 atoms in 400 residues

Initialising van der waals distances...
Will generate new solvent configuration of 1x2x1 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
MeOH ( 3 atoms): 800 residues
Calculating Overlap...
box_margin = 0.315
Removed 609 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48
Generated table with 0 data points for COUL.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 0 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 2591 charge groups and 2591 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Grid: 12 x 19 x 10 cells
Succesfully made neighbourlist
nri = 4450, nrj = 50057
Checking Protein-Solvent overlap: tested 1864 pairs, removed 162 atoms.
Checking Solvent-Solvent overlap: tested 11554 pairs, removed 255 atoms.
Added 458 molecules
Generated solvent containing 1374 atoms in 458 residues
Writing generated configuration to b4em.gro
Go Rough, Oppose Many Angry Chinese Serial killers

Output configuration contains 1565 atoms in 477 residues
Volume : 34.9038 (nm^3)
Density : 731.971 (g/l)
Number of SOL molecules: 0



Alok jain
Indian Institute of Tecnology
Kanpur, India




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Alok Jain
2004-09-29 13:29:38 UTC
Permalink
Hello
Nuno
Thanks for advise.i did the same.
#include "ffG43a1.itp"
#include "/home/lysine/methanol/sim/methanol_WFG.itp"
and at the tail of .top file
[ molecules ]
; Compound #mols
Protein 1
Methanol 458 (same as .itp file)

I also made some changes in full.mdp file.
i changed the group name SOL to Methanol for both tc-grps and for
energygrps.But it gave me as like:

Fatal error: Group Methanol not found in indexfile

after that i changed it to MeOH, now it is working fine but still i am
getting 3 warnings.

here i am attaching output of grompp:-

checking input for internal consistency...
calling /lib/cpp...
processing topology...
WARNING 1 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 3]:
Overriding atomtype OMET
WARNING 2 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 4]:
Overriding atomtype CMET
Generated 329 of the 1275 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for Methanol 458
turning all bonds into constraints...
WARNING 3 [file "speptide.top", line 1225]:
System has non-zero total charge: -1.342595e-05

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
# G96ANGLES: 1108
# PDIHS: 510
# IDIHS: 430
# LJ14: 948
# CONSTR: 4698
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
There are: 458 OTHER residues
There are: 19 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
Not using any simulated annealing
Making dummy/rest group for Acceleration containing 1565 elements
Making dummy/rest group for Freeze containing 1565 elements
Making dummy/rest group for VCM containing 1565 elements
Number of degrees of freedom in T-Coupling group Protein is 380.63 Number
of degrees of freedom in T-Coupling group MeOH is 2745.37
Making dummy/rest group for User1 containing 1565 elements
Making dummy/rest group for User2 containing 1565 elements
Making dummy/rest group for XTC containing 1565 elements
Making dummy/rest group for Or. Res. Fit containing 1565 elements
T-Coupling has 2 element(s): Protein MeOH
Energy Mon. has 2 element(s): Protein MeOH
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
Checking consistency between energy and charge groups...
writing run input file...
There were 3 warnings

gcq#196: "Clickety Clickety Click" (System Manager From Hell)


now what are the possibilities for these warnings,
i want to sort out them also,so
can u please suggest me something again.

thanks !
Alok
Post by Nuno R. L. Ferreira
Hi Alok
IIRC, now you just have to edit your topology file by hand.
Right under the #include describing the peptide, put the .itp of methanol.
; Include forcefield parameters
#include "ffG43a1.itp"
#include "meoh_wfg.itp" ; check the .itp name
and at the tail of your .top file, add one line with specifying the
number of methanol molecules added to the system.
Post by Nuno R. L. Ferreira
Methanol 458 ; check the name of [ moleculetype ] under .itp
And you're done.
Best regards.
Nuno
Nuno R. L. Ferreira
2004-09-29 14:51:17 UTC
Permalink
checking input for internal consistency...
calling /lib/cpp...
processing topology...
WARNING 1 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 3]:
Overriding atomtype OMET
WARNING 2 [file "/home/lysine/methanol/sim/methanol_WFG.itp", line 4]:
Overriding atomtype CMET
Generated 329 of the 1275 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for Methanol 458
turning all bonds into constraints...
WARNING 3 [file "speptide.top", line 1225]:
System has non-zero total charge: -1.342595e-05

Hi Alok

These *warnings* are not errors, at least I think.
If you check the ffG41.atp file, you will find there OMET and CMET already
defined.
So, what I think its happening, is that grompp see two OMET's and two CMET's
parameters, the ones already incorporated in the gromos43a1 f.f. and in the
....WFG.itp file.
I do not know which parameters are attributed to methanol-other atoms
interactions.
I think you could rename atom types in the methanol_WFG.itp like this:

[ atomtypes ]
; type mass charge ptype c6 c12
OMET1 15.999 0.0000 A 2.26576e-3 2.325625e-6
CMET1 15.035 0.0000 A 8.87364e-3 1.936000e-5
HO 1.008 0.0000 A 0.0 0.0

[ moleculetype ]
; name nrexcl
Methanol 2

[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CMET1 1 MeOH Me1 1 0.266000 15.035
2 OMET1 1 MeOH O2 1 -0.674000 15.999
3 HO 1 MeOH H3 1 0.408000 1.008

[ constraints ]
; ai aj funct c0
1 2 1 0.15300
2 3 1 0.10000
1 3 1 0.20770

[ exclusions ]
; ai aj ak
1 2 3
2 3 1
3 2 1

;Model "B3" from W.F. van Gunsteren et.al., JCP 112, 2000, 10450
;Christoph Freudenberger 13/03/03
;
; Edited the following atom types:
; CMET --> CMET1
; OMET --> OMET1 , Nuno R.L. Ferreira 29set04

This way I think you will not get those warnings.
About the charge warning, 10-5 is nothing. Think its roundoff errors.

Regards,
Nuno

P.S. If this protocol is wrong, please could someone shed some light on
this?
David van der Spoel
2004-09-30 06:56:20 UTC
Permalink
Post by Alok Jain
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Overriding atomtype OMET
Overriding atomtype CMET
Generated 329 of the 1275 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for Methanol 458
turning all bonds into constraints...
System has non-zero total charge: -1.342595e-05
Hi Alok
These *warnings* are not errors, at least I think.
If you check the ffG41.atp file, you will find there OMET and CMET already
defined.
That's correct.
So the message said that previsouly defined values for OMET and CMET are
replace by the new ones. Make sure which ones you want (by checking the
literature) and (most likely) you will want to remove the values from
the methanol.itp file (or the force field file if you decide otherwise).
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Alok
2004-09-30 09:25:40 UTC
Permalink
Hello Dr. david & Dr.nuno,
Thanks for your suggesions.
As Dr.nuno suggested,i made some changes in .top file so now its
working fine without any warning.
Now i want to know that how can i use parameters for methanol,define in
force field?
If i dont change the atom name than it will take value specify in
methanol.itp file(as i think) and if i change atom name OMET to OMET1
and CMET to CMET1 than also it takes the value of methanol.itp.so suggest
me if i want to take parameters define in gromax force field than
what i have to do? thanks.
Alok jain
Post by David van der Spoel
Post by Alok Jain
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Overriding atomtype OMET
Overriding atomtype CMET
Generated 329 of the 1275 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for Methanol 458
turning all bonds into constraints...
System has non-zero total charge: -1.342595e-05
Hi Alok
These *warnings* are not errors, at least I think.
If you check the ffG41.atp file, you will find there OMET and CMET already
defined.
That's correct.
So the message said that previsouly defined values for OMET and CMET are
replace by the new ones. Make sure which ones you want (by checking the
literature) and (most likely) you will want to remove the values from
the methanol.itp file (or the force field file if you decide otherwise).
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel
2004-09-30 09:37:59 UTC
Permalink
Post by Alok
Hello Dr. david & Dr.nuno,
Thanks for your suggesions.
As Dr.nuno suggested,i made some changes in .top file so now its
working fine without any warning.
Now i want to know that how can i use parameters for methanol,define in
force field?
If i dont change the atom name than it will take value specify in
methanol.itp file(as i think) and if i change atom name OMET to OMET1
and CMET to CMET1 than also it takes the value of methanol.itp.so suggest
me if i want to take parameters define in gromax force field than
what i have to do? thanks.
Alok jain
remove the atomtypes definition from the methanol.itp file.
Post by Alok
Post by David van der Spoel
Post by Alok Jain
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Overriding atomtype OMET
Overriding atomtype CMET
Generated 329 of the 1275 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for Methanol 458
turning all bonds into constraints...
System has non-zero total charge: -1.342595e-05
Hi Alok
These *warnings* are not errors, at least I think.
If you check the ffG41.atp file, you will find there OMET and CMET already
defined.
That's correct.
So the message said that previsouly defined values for OMET and CMET are
replace by the new ones. Make sure which ones you want (by checking the
literature) and (most likely) you will want to remove the values from
the methanol.itp file (or the force field file if you decide otherwise).
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Alok
2004-09-30 12:04:42 UTC
Permalink
Hello
As i generated the pdb file of tripeptide (GPG) using insight. After
capping (neuralising) of that peptide on both N and C terminal (i changed
glycine?s N terminal to NH2 and second glycine?s C terminal to COOH).
But now i am geeting another problem as these GLY residues are not define
in .rtp file.so following error comes up after pdb2gmx.




Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 124 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 124 atoms

chain #res #atoms
1 ' ' 16 124

WARNING: there were 0 atoms with zero occupancy and 1 atoms with
occupancy unequal to one (out of 124 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up peptide.top to ./#peptide.top.7#
Processing chain 1 (124 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Fatal error: Atom HA1 in residue GLY 1 not found in rtp entry with 5 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.




so now what I have to do now? should i define these GLY residue in .rtp
file?? Or anything else??

i am attaching pdb file also.




ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O OH 2 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO OH 2 13.391 36.273 29.966 1.00 0.00
H



Thanks!

Alok
David van der Spoel
2004-09-30 12:16:04 UTC
Permalink
Post by Alok
Hello
As i generated the pdb file of tripeptide (GPG) using insight. After
capping (neuralising) of that peptide on both N and C terminal (i changed
glycines N terminal to NH2 and second glycines C terminal to COOH).
But now i am geeting another problem as these GLY residues are not define
in .rtp file.so following error comes up after pdb2gmx.
pdb2gmx -ter -ignh
Post by Alok
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 124 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 124 atoms
chain #res #atoms
1 ' ' 16 124
WARNING: there were 0 atoms with zero occupancy and 1 atoms with
occupancy unequal to one (out of 124 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb
Back Off! I just backed up peptide.top to ./#peptide.top.7#
Processing chain 1 (124 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Fatal error: Atom HA1 in residue GLY 1 not found in rtp entry with 5 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.
so now what I have to do now? should i define these GLY residue in .rtp
file?? Or anything else??
i am attaching pdb file also.
ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O OH 2 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO OH 2 13.391 36.273 29.966 1.00 0.00
H
Thanks!
Alok
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--
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Alok
2004-09-30 12:54:32 UTC
Permalink
Hello
Thanks for your suggestion.
i used that options but now i am getting following Fatal error.
i used pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro -p peptide.top




Opening library file /usr/local/share/gromacs/top/FF.dat

Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 64 atoms

chain #res #atoms
1 ' ' 16 64

WARNING: there were 1 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 64 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up peptide.top to ./#peptide.top.16#
Processing chain 1 (64 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Checking for duplicate atoms....
Select N-terminus type (start)
0: GLY-NH3+
1: NH2
2: None
1
N-terminus: NH2
Select C-terminus type (end)
0: COO-
1: COOH
2: None
1
C-terminus: COOH
Fatal error: Atom C not found in residue GLY16 while adding hydrogens




My PDB file :-


ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 2 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 2 13.391 36.273 29.966 1.00 0.00
H
TER
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
TER
ATOM 61 O GLY 2 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 2 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 2 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 2 49.769 90.133 37.898 1.00 0.00
H
TER
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 2 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 2 9.429 86.341 25.523 1.00 0.00
H
END



I also tryied to find out GLY16 residue but i didnt find anywhere in pdb
file.

Thanks!

Alok
David van der Spoel
2004-09-30 13:11:16 UTC
Permalink
Post by Alok
Hello
Thanks for your suggestion.
i used that options but now i am getting following Fatal error.
i used pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro -p peptide.top
your pdb file is severely crippled. you have multiple peptides in it all
marked with labels in the wrong place. get rid of the B's and C's
and put only one peptide in the file.
Post by Alok
Opening library file /usr/local/share/gromacs/top/FF.dat
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 64 atoms
chain #res #atoms
1 ' ' 16 64
WARNING: there were 1 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 64 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb
Back Off! I just backed up peptide.top to ./#peptide.top.16#
Processing chain 1 (64 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Checking for duplicate atoms....
Select N-terminus type (start)
0: GLY-NH3+
1: NH2
2: None
1
N-terminus: NH2
Select C-terminus type (end)
0: COO-
1: COOH
2: None
1
C-terminus: COOH
Fatal error: Atom C not found in residue GLY16 while adding hydrogens
My PDB file :-
ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 2 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 2 13.391 36.273 29.966 1.00 0.00
H
TER
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
TER
ATOM 61 O GLY 2 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 2 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 2 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 2 49.769 90.133 37.898 1.00 0.00
H
TER
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 2 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 2 9.429 86.341 25.523 1.00 0.00
H
END
I also tryied to find out GLY16 residue but i didnt find anywhere in pdb
file.
Thanks!
Alok
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Alok
2004-09-30 17:28:28 UTC
Permalink
Hello
sorry to bother you again, sir!
I think there is some confusion regarding the simulation that I am doing.
So, I am describing again and it is as follows:
I am trying to simulate four triplet peptides (Gly1-Pro-Gly2).
I have generated all the four peptides using InsightII and all
the four have different x,y and z coordinates.Also , I have
done the clipping of each peptides (i.e. NH2 in Gly1 and COOH
in Gly2). Then I have generated a pdb file in which all these
peptides are very far away from each other(in the sense of
coordinates).
when i used pdb2gmx -ignh -f peptide.pdb -o peptide.gro -p peptide.top
it genrates .gro and .top file but it also creates the bond between all
four peptides (which i dont want)
So, is there any option in gromacs to keep all these peptides seperately
as different seqments without creating peptide bond between them. (like
the "segment" flag in CHARMM)
I also checked it with pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro
-p peptide.top but there too, the problem is same.

If I am not wrong then Dr. Peter Tieleman did the same with four
Alamethicin Helices using gromacs.

Kindly suggest me as to what is the alternative and how to proceed further.

Regards,
Alok



output of the pdb2gmx program is as follows:



Opening library file /usr/local/share/gromacs/top/FF.dat

Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 12 residues with 64 atoms

chain #res #atoms
1 ' ' 12 64

All occupancies are one
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up peptidetest.top to ./#peptidetest.top.6#
Processing chain 1 (64 atoms, 12 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 20 hydrogen bonds
Checking for duplicate atoms....
deleting duplicate atom O GLY 3 pdb nr 30
deleting duplicate atom O GLY 6 pdb nr 61
deleting duplicate atom O GLY 9 pdb nr 92
deleting duplicate atom O GLY 12 pdb nr 123
Now there are 60 atoms
N-terminus: GLY-NH3+
C-terminus: COO-
Now there are 12 residues with 71 atoms
Making bonds...
Warning: Long Bond (18-20 = 4.40022 nm)
Warning: Long Bond (35-37 = 4.04127 nm)
Warning: Long Bond (52-54 = 4.36763 nm)
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Number of bonds was 79, now 74
Generating angles, dihedrals and pairs...
Before cleaning: 113 pairs
Before cleaning: 133 dihedrals
There are 51 dihedrals, 27 impropers, 107 angles
113 pairs, 74 bonds and 0 dummies
Total mass 862.901 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.5#

Writing coordinate file...

Back Off! I just backed up peptide.gro to ./#peptide.gro.4#
--------- PLEASE NOTE ------------
You have succesfully generated a topology from: peptide.pdb.
The select force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
--------- ETON ESAELP ------------

gcq#247: "Uh-oh" (Tinky Winky)




my PDB file :-


REMARK 4
REMARK 4 FINA COMPLIES WITH FORMAT V. 2.0, 30-SEP-2004
ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 1C 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 1C 13.391 36.273 29.966 1.00 0.00
H
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
ATOM 61 O GLY 1C 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 1C 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 1C 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 1C 49.769 90.133 37.898 1.00 0.00
H
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 1C 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 1C 9.429 86.341 25.523 1.00 0.00
H
END
Nuno R. L. Ferreira
2004-09-30 17:51:34 UTC
Permalink
----- Original Message -----
From: "Alok" <alokjain at iitk.ac.in>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, September 30, 2004 6:28 PM
Subject: Re: [gmx-users] Capping (neuralising) of peptide


Hello
sorry to bother you again, sir!
I think there is some confusion regarding the simulation that I am doing.
So, I am describing again and it is as follows:
I am trying to simulate four triplet peptides (Gly1-Pro-Gly2).

So, just forget what I said.
I remember someone was asking about multiple peptides, in the e-mail list.
I think that what people uasually do (never done though), is to give a
different chain for each peptide (A, B,C,D for e.g.). In the pdb uploaded
in your previous e-mail, there was no chain id.
Pdb2gmx deals with multiple chains.
I don't know if its better to split your pdb into 4 pieces, one for each
tripeptide and create 4 topologies and merge them afterwards, or to use one
pdb with 4 chains of your peptide.

NUno


I have generated all the four peptides using InsightII and all
the four have different x,y and z coordinates.Also , I have
done the clipping of each peptides (i.e. NH2 in Gly1 and COOH
in Gly2). Then I have generated a pdb file in which all these
peptides are very far away from each other(in the sense of
coordinates).
when i used pdb2gmx -ignh -f peptide.pdb -o peptide.gro -p peptide.top
it genrates .gro and .top file but it also creates the bond between all
four peptides (which i dont want)
So, is there any option in gromacs to keep all these peptides seperately
as different seqments without creating peptide bond between them. (like
the "segment" flag in CHARMM)
I also checked it with pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro
-p peptide.top but there too, the problem is same.

If I am not wrong then Dr. Peter Tieleman did the same with four
Alamethicin Helices using gromacs.

Kindly suggest me as to what is the alternative and how to proceed further.

Regards,
Alok



output of the pdb2gmx program is as follows:



Opening library file /usr/local/share/gromacs/top/FF.dat

Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) 3:
OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 12 residues with 64 atoms

chain #res #atoms
1 ' ' 12 64

All occupancies are one
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up peptidetest.top to ./#peptidetest.top.6#
Processing chain 1 (64 atoms, 12 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 20 hydrogen bonds
Checking for duplicate atoms....
deleting duplicate atom O GLY 3 pdb nr 30
deleting duplicate atom O GLY 6 pdb nr 61
deleting duplicate atom O GLY 9 pdb nr 92
deleting duplicate atom O GLY 12 pdb nr 123
Now there are 60 atoms
N-terminus: GLY-NH3+
C-terminus: COO-
Now there are 12 residues with 71 atoms
Making bonds...
Warning: Long Bond (18-20 = 4.40022 nm)
Warning: Long Bond (35-37 = 4.04127 nm)
Warning: Long Bond (52-54 = 4.36763 nm)
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Number of bonds was 79, now 74
Generating angles, dihedrals and pairs...
Before cleaning: 113 pairs
Before cleaning: 133 dihedrals
There are 51 dihedrals, 27 impropers, 107 angles
113 pairs, 74 bonds and 0 dummies
Total mass 862.901 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.5#

Writing coordinate file...

Back Off! I just backed up peptide.gro to ./#peptide.gro.4#
--------- PLEASE NOTE ------------
You have succesfully generated a topology from: peptide.pdb.
The select force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
--------- ETON ESAELP ------------

gcq#247: "Uh-oh" (Tinky Winky)




my PDB file :-


REMARK 4
REMARK 4 FINA COMPLIES WITH FORMAT V. 2.0, 30-SEP-2004
ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 1C 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 1C 13.391 36.273 29.966 1.00 0.00
H
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
ATOM 61 O GLY 1C 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 1C 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 1C 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 1C 49.769 90.133 37.898 1.00 0.00
H
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 1C 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 1C 9.429 86.341 25.523 1.00 0.00
H
END





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Nuno R. L. Ferreira
2004-09-30 13:03:08 UTC
Permalink
Yap, David's right.
If I recall, you talked about a tripeptide, and you are getting 16 residues.

----- Original Message -----
From: "Alok" <alokjain at iitk.ac.in>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, September 30, 2004 1:54 PM
Subject: Re: [gmx-users] Capping (neuralising) of peptide


Hello
Thanks for your suggestion.
i used that options but now i am getting following Fatal error.
i used pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro -p peptide.top




Opening library file /usr/local/share/gromacs/top/FF.dat

Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 64 atoms

chain #res #atoms
1 ' ' 16 64

WARNING: there were 1 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 64 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up peptide.top to ./#peptide.top.16#
Processing chain 1 (64 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Checking for duplicate atoms....
Select N-terminus type (start)
0: GLY-NH3+
1: NH2
2: None
1
N-terminus: NH2
Select C-terminus type (end)
0: COO-
1: COOH
2: None
1
C-terminus: COOH
Fatal error: Atom C not found in residue GLY16 while adding hydrogens




My PDB file :-


ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 2 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 2 13.391 36.273 29.966 1.00 0.00
H
TER
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
TER
ATOM 61 O GLY 2 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 2 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 2 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 2 49.769 90.133 37.898 1.00 0.00
H
TER
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 2 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 2 9.429 86.341 25.523 1.00 0.00
H
END



I also tryied to find out GLY16 residue but i didnt find anywhere in pdb
file.

Thanks!

Alok



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Nuno R. L. Ferreira
2004-09-30 13:14:12 UTC
Permalink
Alok

You are gettting 16 residues because you have chunks of 4 residues (between
TER tags) repeated 4 times (till END tag). The fourth residue is in the
C-terminal (GLY 2 in your pdb).
My guess is that is played around with insight, but forgot to delete
previous molecules created.
Create your tripeptite , and as David implicitely said, do not worry about
the terminals, cause you can cap them under pdb2gmx.


----- Original Message -----
From: "Alok" <alokjain at iitk.ac.in>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, September 30, 2004 1:54 PM
Subject: Re: [gmx-users] Capping (neuralising) of peptide


Hello
Thanks for your suggestion.
i used that options but now i am getting following Fatal error.
i used pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro -p peptide.top




Opening library file /usr/local/share/gromacs/top/FF.dat

Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 64 atoms

chain #res #atoms
1 ' ' 16 64

WARNING: there were 1 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 64 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb

Back Off! I just backed up peptide.top to ./#peptide.top.16#
Processing chain 1 (64 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Checking for duplicate atoms....
Select N-terminus type (start)
0: GLY-NH3+
1: NH2
2: None
1
N-terminus: NH2
Select C-terminus type (end)
0: COO-
1: COOH
2: None
1
C-terminus: COOH
Fatal error: Atom C not found in residue GLY16 while adding hydrogens




My PDB file :-


ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 2 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 2 13.391 36.273 29.966 1.00 0.00
H
TER
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
TER
ATOM 61 O GLY 2 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 2 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 2 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 2 49.769 90.133 37.898 1.00 0.00
H
TER
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 2 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 2 9.429 86.341 25.523 1.00 0.00
H
END



I also tryied to find out GLY16 residue but i didnt find anywhere in pdb
file.

Thanks!

Alok



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