Discussion:
bad bond in polymer
(too old to reply)
nicegromacs
2009-08-13 00:28:30 UTC
Permalink
Hi gmx-users,

I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer.
How can I prevent the monomers at the end forming the bond?

I have read other post like http://www.mail-archive.com/gmx-users at gromacs.org/msg21133.html but can not avoid this problem .

Thank you in advance

veduardo.

Lab. de Fisicoqu?mica Molecular

Facultas de Ciencias

Universidad de Chile




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Justin A. Lemkul
2009-08-13 00:36:21 UTC
Permalink
Post by nicegromacs
Hi gmx-users,
I am building a polymer and I've added the monomer unit to the
.rtp file. The final structure appears with an undesired bond between
the monomer units at the extremes of the polymer.
How can I prevent the monomers at the end forming the bond?
Bonds that appear in visualization software are separate from bonds that exist
in the topology. Programs like VMD guess where bonds should be based on atomic
distances, which may or may not correspond to reality.

Be assured that the only true bonds are the ones you have defined in the topology.

-Justin
Post by nicegromacs
I have read other post like
http://www.mail-archive.com/gmx-users at gromacs.org/msg21133.html but
can not avoid this problem .
Thank you in advance
veduardo.
Lab. de Fisicoqu?mica Molecular
Facultas de Ciencias
Universidad de Chile
------------------------------------------------------------------------
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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

========================================
nicegromacs
2009-08-13 01:21:18 UTC
Permalink
Hi,

the bad bond appear in the topology (.top) file.

veduardo.

Lab. de Fisicoqu?mica Molecular

Facultas de Ciencias

Universidad de Chile


From: nicegromacs
Sent: Wednesday, August 12, 2009 8:28 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] bad bond in polymer


Hi gmx-users,

I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer.
How can I prevent the monomers at the end forming the bond?

I have read other post like http://www.mail-archive.com/gmx-users at gromacs.org/msg21133.html but can not avoid this problem .

Thank you in advance

veduardo.

Lab. de Fisicoqu?mica Molecular

Facultas de Ciencias

Universidad de Chile







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


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Justin A. Lemkul
2009-08-13 01:23:16 UTC
Permalink
Post by nicegromacs
Hi,
the bad bond appear in the topology (.top) file.
Then it is something you have added. If you want any useful advice, post the
.rtp entries you are using.

-Justin
Post by nicegromacs
veduardo.
Lab. de Fisicoqu?mica Molecular
Facultas de Ciencias
Universidad de Chile
*From:* nicegromacs <mailto:nicegromacs at live.cl>
*Sent:* Wednesday, August 12, 2009 8:28 PM
*To:* gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
*Subject:* [gmx-users] bad bond in polymer
Hi gmx-users,
I am building a polymer and I've added the monomer unit to the
.rtp file. The final structure appears with an undesired bond between
the monomer units at the extremes of the polymer.
How can I prevent the monomers at the end forming the bond?
I have read other post like
http://www.mail-archive.com/gmx-users at gromacs.org/msg21133.html but
can not avoid this problem .
Thank you in advance
veduardo.
Lab. de Fisicoqu?mica Molecular
Facultas de Ciencias
Universidad de Chile
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://lists.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://lists.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

========================================
nicegromacs
2009-08-13 01:29:51 UTC
Permalink
Hi,
the .rtp

[ POL ]
[ atoms ]
CAA CH3 0.000
CAB CH2 0.000
CAC CH2 0.000
CAD CH2 0.000
CAE CH2 0.000
CAF CH2 0.000
CAG CH1 0.000
CAH CH2 0.041
CAI CH1 0.107
CAJ C 0.352
OAK OM -0.750
OAL OM -0.750
CAM CH2 0.044
CAN C 0.373
OAO OM -0.709
OAP OM -0.708
[ bonds ]
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
CAG -CAM
[ impropers ]
CAG CAF -CAM CAH
-CAM -CAN -CAI CAG
CAJ CAI OAL OAK
CAN CAM OAP OAO
CAI CAH CAJ CAM

--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Wednesday, August 12, 2009 9:23 PM
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
Hi,
the bad bond appear in the topology (.top) file.
Then it is something you have added. If you want any useful advice, post
the .rtp entries you are using.
-Justin
Post by nicegromacs
veduardo.
Lab. de Fisicoqu?mica Molecular
Facultas de Ciencias
Universidad de Chile
*From:* nicegromacs <mailto:nicegromacs at live.cl>
*Sent:* Wednesday, August 12, 2009 8:28 PM
*To:* gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
*Subject:* [gmx-users] bad bond in polymer
Hi gmx-users,
I am building a polymer and I've added the monomer unit to the .rtp file.
The final structure appears with an undesired bond between the monomer
units at the extremes of the polymer.
How can I prevent the monomers at the end forming the bond?
I have read other post like
http://www.mail-archive.com/gmx-users at gromacs.org/msg21133.html but can
not avoid this problem .
Thank you in advance
veduardo.
Lab. de Fisicoqu?mica Molecular
Facultas de Ciencias
Universidad de Chile
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://lists.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://lists.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://lists.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
2009-08-13 01:50:41 UTC
Permalink
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least one
terminus of your polymer chain. You may find this post useful:

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

If things still aren't working, please post the structure file, as well, and
identify the bond that is being formed that shouldn't.

-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

========================================
nicegromacs
2009-08-13 03:57:13 UTC
Permalink
Well, I tried to build a polymer with 3 monomers, DRG DR0 and DR1. In the
pdb file They have the same order (DRG DR0 DR1). But when tried with
pdb2gmx then I have the error:
Fatal error:
In the .rtp file in residue DR1 at line:
CF1 CH3 0 1
I changed the order of monomers to DR0 DRG DR1 with respect to the ''head''
monomer (DR0), Monomer of in the middle (DRG), and tail monomer (DR1), and
the error no change. I have not changed the .hdb file.

the estructure.ent
HETATM 1 CAA DRG 1 58.110 44.852 36.809
HETATM 2 CAB DRG 1 56.934 44.517 35.875
HETATM 3 CAC DRG 1 56.190 45.811 35.500
HETATM 4 CAD DRG 1 55.051 45.476 34.520
HETATM 5 CAE DRG 1 54.318 46.770 34.118
HETATM 6 CAF DRG 1 53.310 46.438 33.003
HETATM 7 CAG DRG 1 52.657 47.686 32.473
HETATM 8 CAH DRG 1 53.521 48.753 31.851
HETATM 9 CAI DRG 1 54.199 48.265 30.599
HETATM 10 CAJ DRG 1 55.615 47.887 30.630
HETATM 11 OAK DRG 1 56.231 47.370 29.495
HETATM 12 OAL DRG 1 56.359 48.028 31.798
HETATM 13 CAM DRG 1 53.423 48.169 29.314
HETATM 14 CAN DRG 1 52.529 46.963 29.306
HETATM 15 OAO DRG 1 53.058 45.698 29.542
HETATM 16 OAP DRG 1 51.206 47.090 28.902
HETATM 17 CA1 DR0 1 43.743 50.975 25.947
HETATM 18 CA2 DR0 1 44.674 51.739 26.906
HETATM 19 CA3 DR0 1 45.313 50.749 27.897
HETATM 20 CA4 DR0 1 46.248 51.508 28.856
HETATM 21 CA5 DR0 1 46.862 50.512 29.856
HETATM 22 CA6 DR0 1 47.789 51.264 30.830
HETATM 23 CA7 DR0 1 48.356 50.315 31.851
HETATM 24 CA8 DR0 1 49.361 49.293 31.385
HETATM 25 CA9 DR0 1 50.545 49.110 32.302
HETATM 26 C10 DR0 1 51.122 50.259 33.020
HETATM 27 O12 DR0 1 50.919 51.560 32.571
HETATM 28 O11 DR0 1 51.877 50.069 34.174
HETATM 29 C13 DR0 1 51.189 47.782 32.378
HETATM 30 C14 DR0 1 50.382 46.559 32.210
HETATM 31 O16 DR0 1 50.972 45.336 31.910
HETATM 32 O15 DR0 1 48.997 46.595 32.315
HETATM 33 CF1 DR1 1 55.642 46.172 39.128
HETATM 34 CF2 DR1 1 54.229 46.780 39.194
HETATM 35 CF3 DR1 1 53.591 46.765 37.791
HETATM 36 CF4 DR1 1 52.185 47.384 37.876
HETATM 37 CF5 DR1 1 51.526 47.395 36.484
HETATM 38 CF6 DR1 1 50.134 48.044 36.601
HETATM 39 CF7 DR1 1 49.475 48.098 35.212
HETATM 40 CF8 DR1 1 48.132 48.846 35.298
HETATM 41 CF9 DR1 1 47.562 49.035 33.918
HETATM 42 C1F DR1 1 46.647 48.028 33.366
HETATM 43 O3F DR1 1 46.397 46.849 34.062
HETATM 44 O2F DR1 1 45.998 48.241 32.154
HETATM 45 C4F DR1 1 47.798 50.304 33.215
HETATM 46 C5F DR1 1 47.426 51.565 33.874
HETATM 47 O7F DR1 1 47.843 52.791 33.365
HETATM 48 O6F DR1 1 46.661 51.551 35.036
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4 6
CONECT 6 5 7
CONECT 7 6 8 29
CONECT 8 7 9
CONECT 9 8 10 13
CONECT 10 9 11 12
CONECT 11 10
CONECT 12 10
CONECT 13 9 14
CONECT 14 13 15 16
CONECT 15 14
CONECT 16 14
CONECT 17 18
CONECT 18 17 19
CONECT 19 18 20
CONECT 20 19 21
CONECT 21 20 22
CONECT 22 21 23
CONECT 23 22 24 45
CONECT 24 23 25
CONECT 25 24 26 29
CONECT 26 25 27 28
CONECT 27 26
CONECT 28 26
CONECT 29 25 30 7
CONECT 30 29 31 32
CONECT 31 30
CONECT 32 30
CONECT 33 34
CONECT 34 33 35
CONECT 35 34 36
CONECT 36 35 37
CONECT 37 36 38
CONECT 38 37 39
CONECT 39 38 40
CONECT 40 39 41
CONECT 41 40 42 45
CONECT 42 41 43 44
CONECT 43 42
CONECT 44 42
CONECT 45 41 46 23
CONECT 46 45 47 48
CONECT 47 46
CONECT 48 46
END
and the .rtp

[ DRG ] ; unidad
[ atoms ]
CAA CH3 0.00
CAB CH2 0.00
CAC CH2 0.00
CAD CH2 0.00
CAE CH2 0.00
CAF CH2 0.00
CAG CH1 0.00
CAH CH2 0.04
CAI CH1 0.10
CAJ C 0.35
OAK OM -0.75
OAL OM -0.75
CAM CH2 0.04
CAN C 0.37
OAO OM -0.70
OAP OM -0.70
[ bonds ]
CAM -CAG
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
CAG +CAM
[ impropers ]
CAG CAF -CAM C
-CAM -CAN -CAI C
CAJ CAI OAL O
CAN CAM OAP O
CAI CAH CAJ C

[ DR0 ] ;head of
[ atoms ]
CA1 CH3 0.00
CA2 CH2 0.00
CA3 CH2 0.00
CA4 CH2 0.00
CA5 CH2 0.00
CA6 CH2 0.00
CA7 CH2 0.00
CA8 CH2 0.04
CA9 CH1 0.10
C10 C 0.35
O12 OM -0.75
O11 OM -0.75
C13 CH2 0.04
C14 C 0.37
O16 OM -0.70
O15 OM -0.70
[ bonds ]
CA1 CA2
CA2 CA3
CA3 CA4
CA4 CA5
CA5 CA6
CA6 CA7
CA7 CA8
CA8 CA9
CA9 C10
CA9 C13
C10 O12
C10 O11
C13 C14
C14 O16
C14 O15
CA7 +CAM
[ impropers ]
CA7 CA6 +CAM CA8
+CAM +CAI +CAN CA7
C10 CA9 O11 O12
C14 C13 O15 O16
CA9 CA8 C10 C13

[ DR1 ] ; tail of t
CF1 CH3 0.00
CF2 CH2 0.00
CF3 CH2 0.00
CF4 CH2 0.00
CF5 CH2 0.00
CF6 CH2 0.00
CF7 CH2 0.00
CF8 CH2 0.04
CF9 CH1 0.10
C1F C 0.35
O3F OM -0.75
O2F OM -0.75
C4F CH2 0.04
C5F C 0.37
O7F OM -0.70
O6F OM -0.70
[ bonds ]
C4F -CAG
CF1 CF2
CF2 CF3
CF3 CF4
CF4 CF5
CF5 CF6
CF6 CF7
CF7 CF8
CF8 CF9
CF9 C1F
CF9 C4F
C1F O3F
C1F O2F
C4F C5F
C5F O7F
C5F O6F
[ impropers ]
C4F C5F CF9 -CAG
-CAG -CAF -CAH C4F
C1F CF9 O2F O3F
C5F C4F O6F O7F
CF9 CF8 C1F C4F


--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Wednesday, August 12, 2009 9:50 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least one
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as well,
and identify the bond that is being formed that shouldn't.
-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://lists.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
Mark Abraham
2009-08-13 04:08:30 UTC
Permalink
Post by nicegromacs
Well, I tried to build a polymer with 3 monomers, DRG DR0 and DR1. In
the pdb file They have the same order (DRG DR0 DR1). But when tried
CF1 CH3 0 1
There is no such line in the .rtp you provided. GROMACS would normally
provide more diagnostic information than this. Are you reading it all?
Are you using the right .rtp files?
Post by nicegromacs
I changed the order of monomers to DR0 DRG DR1 with respect to the
''head'' monomer (DR0), Monomer of in the middle (DRG), and tail monomer
(DR1), and the error no change. I have not changed the .hdb file.
the estructure.ent
HETATM 1 CAA DRG 1 58.110 44.852 36.809
This first residue listed is named as for your repeating unit. You need
to make sure the residue naming here matches your connectivity plan.

Mark
Post by nicegromacs
HETATM 2 CAB DRG 1 56.934 44.517 35.875
HETATM 3 CAC DRG 1 56.190 45.811 35.500
HETATM 4 CAD DRG 1 55.051 45.476 34.520
HETATM 5 CAE DRG 1 54.318 46.770 34.118
HETATM 6 CAF DRG 1 53.310 46.438 33.003
HETATM 7 CAG DRG 1 52.657 47.686 32.473
HETATM 8 CAH DRG 1 53.521 48.753 31.851
HETATM 9 CAI DRG 1 54.199 48.265 30.599
HETATM 10 CAJ DRG 1 55.615 47.887 30.630
HETATM 11 OAK DRG 1 56.231 47.370 29.495
HETATM 12 OAL DRG 1 56.359 48.028 31.798
HETATM 13 CAM DRG 1 53.423 48.169 29.314
HETATM 14 CAN DRG 1 52.529 46.963 29.306
HETATM 15 OAO DRG 1 53.058 45.698 29.542
HETATM 16 OAP DRG 1 51.206 47.090 28.902
HETATM 17 CA1 DR0 1 43.743 50.975 25.947
HETATM 18 CA2 DR0 1 44.674 51.739 26.906
HETATM 19 CA3 DR0 1 45.313 50.749 27.897
HETATM 20 CA4 DR0 1 46.248 51.508 28.856
HETATM 21 CA5 DR0 1 46.862 50.512 29.856
HETATM 22 CA6 DR0 1 47.789 51.264 30.830
HETATM 23 CA7 DR0 1 48.356 50.315 31.851
HETATM 24 CA8 DR0 1 49.361 49.293 31.385
HETATM 25 CA9 DR0 1 50.545 49.110 32.302
HETATM 26 C10 DR0 1 51.122 50.259 33.020
HETATM 27 O12 DR0 1 50.919 51.560 32.571
HETATM 28 O11 DR0 1 51.877 50.069 34.174
HETATM 29 C13 DR0 1 51.189 47.782 32.378
HETATM 30 C14 DR0 1 50.382 46.559 32.210
HETATM 31 O16 DR0 1 50.972 45.336 31.910
HETATM 32 O15 DR0 1 48.997 46.595 32.315
HETATM 33 CF1 DR1 1 55.642 46.172 39.128
HETATM 34 CF2 DR1 1 54.229 46.780 39.194
HETATM 35 CF3 DR1 1 53.591 46.765 37.791
HETATM 36 CF4 DR1 1 52.185 47.384 37.876
HETATM 37 CF5 DR1 1 51.526 47.395 36.484
HETATM 38 CF6 DR1 1 50.134 48.044 36.601
HETATM 39 CF7 DR1 1 49.475 48.098 35.212
HETATM 40 CF8 DR1 1 48.132 48.846 35.298
HETATM 41 CF9 DR1 1 47.562 49.035 33.918
HETATM 42 C1F DR1 1 46.647 48.028 33.366
HETATM 43 O3F DR1 1 46.397 46.849 34.062
HETATM 44 O2F DR1 1 45.998 48.241 32.154
HETATM 45 C4F DR1 1 47.798 50.304 33.215
HETATM 46 C5F DR1 1 47.426 51.565 33.874
HETATM 47 O7F DR1 1 47.843 52.791 33.365
HETATM 48 O6F DR1 1 46.661 51.551 35.036
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4 6
CONECT 6 5 7
CONECT 7 6 8 29
CONECT 8 7 9
CONECT 9 8 10 13
CONECT 10 9 11 12
CONECT 11 10
CONECT 12 10
CONECT 13 9 14
CONECT 14 13 15 16
CONECT 15 14
CONECT 16 14
CONECT 17 18
CONECT 18 17 19
CONECT 19 18 20
CONECT 20 19 21
CONECT 21 20 22
CONECT 22 21 23
CONECT 23 22 24 45
CONECT 24 23 25
CONECT 25 24 26 29
CONECT 26 25 27 28
CONECT 27 26
CONECT 28 26
CONECT 29 25 30 7
CONECT 30 29 31 32
CONECT 31 30
CONECT 32 30
CONECT 33 34
CONECT 34 33 35
CONECT 35 34 36
CONECT 36 35 37
CONECT 37 36 38
CONECT 38 37 39
CONECT 39 38 40
CONECT 40 39 41
CONECT 41 40 42 45
CONECT 42 41 43 44
CONECT 43 42
CONECT 44 42
CONECT 45 41 46 23
CONECT 46 45 47 48
CONECT 47 46
CONECT 48 46
END
and the .rtp
[ DRG ] ; unidad
[ atoms ]
CAA CH3 0.00
CAB CH2 0.00
CAC CH2 0.00
CAD CH2 0.00
CAE CH2 0.00
CAF CH2 0.00
CAG CH1 0.00
CAH CH2 0.04
CAI CH1 0.10
CAJ C 0.35
OAK OM -0.75
OAL OM -0.75
CAM CH2 0.04
CAN C 0.37
OAO OM -0.70
OAP OM -0.70
[ bonds ]
CAM -CAG
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
CAG +CAM
[ impropers ]
CAG CAF -CAM C
-CAM -CAN -CAI C
CAJ CAI OAL O
CAN CAM OAP O
CAI CAH CAJ C
[ DR0 ] ;head of
[ atoms ]
CA1 CH3 0.00
CA2 CH2 0.00
CA3 CH2 0.00
CA4 CH2 0.00
CA5 CH2 0.00
CA6 CH2 0.00
CA7 CH2 0.00
CA8 CH2 0.04
CA9 CH1 0.10
C10 C 0.35
O12 OM -0.75
O11 OM -0.75
C13 CH2 0.04
C14 C 0.37
O16 OM -0.70
O15 OM -0.70
[ bonds ]
CA1 CA2
CA2 CA3
CA3 CA4
CA4 CA5
CA5 CA6
CA6 CA7
CA7 CA8
CA8 CA9
CA9 C10
CA9 C13
C10 O12
C10 O11
C13 C14
C14 O16
C14 O15
CA7 +CAM
[ impropers ]
CA7 CA6 +CAM CA8
+CAM +CAI +CAN CA7
C10 CA9 O11 O12
C14 C13 O15 O16
CA9 CA8 C10 C13
[ DR1 ] ; tail of t
CF1 CH3 0.00
CF2 CH2 0.00
CF3 CH2 0.00
CF4 CH2 0.00
CF5 CH2 0.00
CF6 CH2 0.00
CF7 CH2 0.00
CF8 CH2 0.04
CF9 CH1 0.10
C1F C 0.35
O3F OM -0.75
O2F OM -0.75
C4F CH2 0.04
C5F C 0.37
O7F OM -0.70
O6F OM -0.70
[ bonds ]
C4F -CAG
CF1 CF2
CF2 CF3
CF3 CF4
CF4 CF5
CF5 CF6
CF6 CF7
CF7 CF8
CF8 CF9
CF9 C1F
CF9 C4F
C1F O3F
C1F O2F
C4F C5F
C5F O7F
C5F O6F
[ impropers ]
C4F C5F CF9 -CAG
-CAG -CAF -CAH C4F
C1F CF9 O2F O3F
C5F C4F O6F O7F
CF9 CF8 C1F C4F
--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Wednesday, August 12, 2009 9:50 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as
well, and identify the bond that is being formed that shouldn't.
-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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Mark Abraham
2009-08-13 04:03:42 UTC
Permalink
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
I don't have any relevant experience, but the quoted .rtp might be using
a technique suited for creating a circular/infinite polymer, which would
cause the present problem. Finite polymers need capping residues, either
explicitly defined, or using the .tdb mechanism. See chapter 5.

Mark
nicegromacs
2009-08-14 15:40:07 UTC
Permalink
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one repeat
unit (R)and tail (T) for the polymer (H-R-T) and this gives ok, but when I
add one more repetitive unit (H-R-R-T) I get the following error:
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Fatal error:
Atom CAM not found in residue 1083339441 while adding improper

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

"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least one
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as well,
and identify the bond that is being formed that shouldn't.
-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://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
2009-08-14 16:14:02 UTC
Permalink
Post by nicegromacs
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok,
but when I add one more repetitive unit (H-R-R-T) I get the following
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue. Can you post
the .pdb file?

-Justin
Post by nicegromacs
"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as
well, and identify the bond that is being formed that shouldn't.
-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://lists.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

========================================
nicegromacs
2009-08-14 18:18:52 UTC
Permalink
Hi Justin,

the pdb file:

HETATM 1 CAA DRG 1 83.043 46.127 36.820
HETATM 2 CAB DRG 1 82.411 45.765 35.421
HETATM 3 CAC DRG 1 81.495 46.822 34.598
HETATM 4 CAD DRG 1 80.621 46.369 33.071
HETATM 5 CAE DRG 1 79.305 47.302 32.172
HETATM 6 CAF DRG 1 77.939 46.749 31.124
HETATM 7 CAG DRG 1 76.264 47.439 30.612
HETATM 8 CAH DRG 1 74.636 46.805 29.962
HETATM 9 CAI DRG 1 72.805 47.674 30.179
HETATM 10 CAJ DRG 1 73.794 48.838 31.123
HETATM 11 OAK DRG 1 74.815 49.342 30.292
HETATM 12 OAL DRG 1 74.592 48.143 32.194
HETATM 13 CAM DRG 1 71.093 47.685 29.486
HETATM 14 CAN DRG 1 71.598 47.212 28.208
HETATM 15 OAO DRG 1 72.440 48.255 27.735
HETATM 16 OAP DRG 1 72.374 46.050 28.399
HETATM 17 CAA DRG 1 72.093 46.197 36.714
HETATM 18 CAB DRG 1 71.418 45.759 35.400
HETATM 19 CAC DRG 1 71.084 46.901 34.417
HETATM 20 CAD DRG 1 70.620 46.251 33.139
HETATM 21 CAE DRG 1 70.650 47.255 32.000
HETATM 22 CAF DRG 1 69.655 46.512 30.955
HETATM 23 CAG DRG 1 69.081 47.504 29.843
HETATM 24 CAH DRG 1 67.208 47.518 29.256
HETATM 25 CAI DRG 1 65.298 47.601 29.691
HETATM 26 CAJ DRG 1 65.629 48.362 30.827
HETATM 27 OAK DRG 1 65.140 49.590 30.429
HETATM 28 OAL DRG 1 64.837 47.815 31.709
HETATM 29 CAM DRG 1 63.041 47.557 29.333
HETATM 30 CAN DRG 1 62.808 47.023 27.931
HETATM 31 OAO DRG 1 63.130 48.142 27.185
HETATM 32 OAP DRG 1 63.560 45.894 27.706
HETATM 33 CAA DRG 1 61.174 46.188 36.668
HETATM 34 CAB DRG 1 60.510 45.777 35.344
HETATM 35 CAC DRG 1 60.221 46.928 34.352
HETATM 36 CAD DRG 1 59.724 46.337 32.998
HETATM 37 CAE DRG 1 60.252 47.307 31.985
HETATM 38 CAF DRG 1 61.089 46.606 30.881
HETATM 39 CAG DRG 1 60.868 47.564 29.740
HETATM 40 CAH DRG 1 58.621 47.652 29.253
HETATM 41 CAI DRG 1 56.328 47.703 29.755
HETATM 42 CAJ DRG 1 55.914 48.516 30.963
HETATM 43 OAK DRG 1 55.050 49.545 30.403
HETATM 44 OAL DRG 1 54.945 47.724 31.565
HETATM 45 CAM DRG 1 54.420 47.478 29.367
HETATM 46 CAN DRG 1 53.587 47.142 27.983
HETATM 47 OAO DRG 1 52.713 48.009 27.325
HETATM 48 OAP DRG 1 53.396 45.805 27.517
HETATM 49 CAA DRG 1 50.257 46.173 36.646
HETATM 50 CAB DRG 1 49.673 45.778 35.270
HETATM 51 CAC DRG 1 49.360 46.939 34.273
HETATM 52 CAD DRG 1 49.270 46.480 32.735
HETATM 53 CAE DRG 1 50.289 47.086 31.602
HETATM 54 CAF DRG 1 51.813 46.713 31.234
HETATM 55 CAG DRG 1 52.487 47.720 29.966
HETATM 56 CAH DRG 1 50.870 47.989 29.178
HETATM 57 CAI DRG 1 48.982 47.816 29.191
HETATM 58 CAJ DRG 1 47.901 48.319 30.192
HETATM 59 OAK DRG 1 47.004 49.132 29.503
HETATM 60 OAL DRG 1 46.963 47.171 30.588
HETATM 61 CAM DRG 1 47.752 46.922 28.157
HETATM 62 CAN DRG 1 46.372 47.149 27.020
HETATM 63 OAO DRG 1 45.018 47.950 26.877
HETATM 64 OAP DRG 1 46.019 46.082 26.137


--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok,
but when I add one more repetitive unit (H-R-R-T) I get the following
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue. Can you
post the .pdb file?
-Justin
Post by nicegromacs
"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as well,
and identify the bond that is being formed that shouldn't.
-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://lists.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://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
2009-08-14 18:20:28 UTC
Permalink
All of your residue numbers are one, so I think pdb2gmx is trying to make them
all one residue. Try giving each unit a sequential residue number.

-Justin
Post by nicegromacs
Hi Justin,
HETATM 1 CAA DRG 1 83.043 46.127 36.820
HETATM 2 CAB DRG 1 82.411 45.765 35.421
HETATM 3 CAC DRG 1 81.495 46.822 34.598
HETATM 4 CAD DRG 1 80.621 46.369 33.071
HETATM 5 CAE DRG 1 79.305 47.302 32.172
HETATM 6 CAF DRG 1 77.939 46.749 31.124
HETATM 7 CAG DRG 1 76.264 47.439 30.612
HETATM 8 CAH DRG 1 74.636 46.805 29.962
HETATM 9 CAI DRG 1 72.805 47.674 30.179
HETATM 10 CAJ DRG 1 73.794 48.838 31.123
HETATM 11 OAK DRG 1 74.815 49.342 30.292
HETATM 12 OAL DRG 1 74.592 48.143 32.194
HETATM 13 CAM DRG 1 71.093 47.685 29.486
HETATM 14 CAN DRG 1 71.598 47.212 28.208
HETATM 15 OAO DRG 1 72.440 48.255 27.735
HETATM 16 OAP DRG 1 72.374 46.050 28.399
HETATM 17 CAA DRG 1 72.093 46.197 36.714
HETATM 18 CAB DRG 1 71.418 45.759 35.400
HETATM 19 CAC DRG 1 71.084 46.901 34.417
HETATM 20 CAD DRG 1 70.620 46.251 33.139
HETATM 21 CAE DRG 1 70.650 47.255 32.000
HETATM 22 CAF DRG 1 69.655 46.512 30.955
HETATM 23 CAG DRG 1 69.081 47.504 29.843
HETATM 24 CAH DRG 1 67.208 47.518 29.256
HETATM 25 CAI DRG 1 65.298 47.601 29.691
HETATM 26 CAJ DRG 1 65.629 48.362 30.827
HETATM 27 OAK DRG 1 65.140 49.590 30.429
HETATM 28 OAL DRG 1 64.837 47.815 31.709
HETATM 29 CAM DRG 1 63.041 47.557 29.333
HETATM 30 CAN DRG 1 62.808 47.023 27.931
HETATM 31 OAO DRG 1 63.130 48.142 27.185
HETATM 32 OAP DRG 1 63.560 45.894 27.706
HETATM 33 CAA DRG 1 61.174 46.188 36.668
HETATM 34 CAB DRG 1 60.510 45.777 35.344
HETATM 35 CAC DRG 1 60.221 46.928 34.352
HETATM 36 CAD DRG 1 59.724 46.337 32.998
HETATM 37 CAE DRG 1 60.252 47.307 31.985
HETATM 38 CAF DRG 1 61.089 46.606 30.881
HETATM 39 CAG DRG 1 60.868 47.564 29.740
HETATM 40 CAH DRG 1 58.621 47.652 29.253
HETATM 41 CAI DRG 1 56.328 47.703 29.755
HETATM 42 CAJ DRG 1 55.914 48.516 30.963
HETATM 43 OAK DRG 1 55.050 49.545 30.403
HETATM 44 OAL DRG 1 54.945 47.724 31.565
HETATM 45 CAM DRG 1 54.420 47.478 29.367
HETATM 46 CAN DRG 1 53.587 47.142 27.983
HETATM 47 OAO DRG 1 52.713 48.009 27.325
HETATM 48 OAP DRG 1 53.396 45.805 27.517
HETATM 49 CAA DRG 1 50.257 46.173 36.646
HETATM 50 CAB DRG 1 49.673 45.778 35.270
HETATM 51 CAC DRG 1 49.360 46.939 34.273
HETATM 52 CAD DRG 1 49.270 46.480 32.735
HETATM 53 CAE DRG 1 50.289 47.086 31.602
HETATM 54 CAF DRG 1 51.813 46.713 31.234
HETATM 55 CAG DRG 1 52.487 47.720 29.966
HETATM 56 CAH DRG 1 50.870 47.989 29.178
HETATM 57 CAI DRG 1 48.982 47.816 29.191
HETATM 58 CAJ DRG 1 47.901 48.319 30.192
HETATM 59 OAK DRG 1 47.004 49.132 29.503
HETATM 60 OAL DRG 1 46.963 47.171 30.588
HETATM 61 CAM DRG 1 47.752 46.922 28.157
HETATM 62 CAN DRG 1 46.372 47.149 27.020
HETATM 63 OAO DRG 1 45.018 47.950 26.877
HETATM 64 OAP DRG 1 46.019 46.082 26.137
--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
(I omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives
ok, but when I add one more repetitive unit (H-R-R-T) I get the
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue. Can
you post the .pdb file?
-Justin
Post by nicegromacs
"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at
least one terminus of your polymer chain. You may find this post
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as
well, and identify the bond that is being formed that shouldn't.
-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://lists.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://lists.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

========================================
nicegromacs
2009-08-14 18:31:59 UTC
Permalink
Hi Justin,

ups!! I am sorry this is the exact .pdb file.

HETATM 1 CAA DR0 1 83.043 46.127 36.820 1.00 0.00
HETATM 2 CAB DR0 1 82.411 45.765 35.421 1.00 0.00
HETATM 3 CAC DR0 1 81.495 46.822 34.598 1.00 0.00
HETATM 4 CAD DR0 1 80.621 46.369 33.071 1.00 0.00
HETATM 5 CAE DR0 1 79.305 47.302 32.172 1.00 0.00
HETATM 6 CAF DR0 1 77.939 46.749 31.124 1.00 0.00
HETATM 7 CAG DR0 1 76.264 47.439 30.612 1.00 0.00
HETATM 8 CAH DR0 1 74.636 46.805 29.962 1.00 0.00
HETATM 9 CAI DR0 1 72.805 47.674 30.179 1.00 0.00
HETATM 10 CAJ DR0 1 73.794 48.838 31.123 1.00 0.00
HETATM 11 OAK DR0 1 74.815 49.342 30.292 1.00 0.00
HETATM 12 OAL DR0 1 74.592 48.143 32.194 1.00 0.00
HETATM 13 CAM DR0 1 71.093 47.685 29.486 1.00 0.00
HETATM 14 CAN DR0 1 71.598 47.212 28.208 1.00 0.00
HETATM 15 OAO DR0 1 72.440 48.255 27.735 1.00 0.00
HETATM 16 OAP DR0 1 72.374 46.050 28.399 1.00 0.00
HETATM 17 CAA DRG 2 72.093 46.197 36.714 1.00 0.00
HETATM 18 CAB DRG 2 71.418 45.759 35.400 1.00 0.00
HETATM 19 CAC DRG 2 71.084 46.901 34.417 1.00 0.00
HETATM 20 CAD DRG 2 70.620 46.251 33.139 1.00 0.00
HETATM 21 CAE DRG 2 70.650 47.255 32.000 1.00 0.00
HETATM 22 CAF DRG 2 69.655 46.512 30.955 1.00 0.00
HETATM 23 CAG DRG 2 69.081 47.504 29.843 1.00 0.00
HETATM 24 CAH DRG 2 67.208 47.518 29.256 1.00 0.00
HETATM 25 CAI DRG 2 65.298 47.601 29.691 1.00 0.00
HETATM 26 CAJ DRG 2 65.629 48.362 30.827 1.00 0.00
HETATM 27 OAK DRG 2 65.140 49.590 30.429 1.00 0.00
HETATM 28 OAL DRG 2 64.837 47.815 31.709 1.00 0.00
HETATM 29 CAM DRG 2 63.041 47.557 29.333 1.00 0.00
HETATM 30 CAN DRG 2 62.808 47.023 27.931 1.00 0.00
HETATM 31 OAO DRG 2 63.130 48.142 27.185 1.00 0.00
HETATM 32 OAP DRG 2 63.560 45.894 27.706 1.00 0.00
HETATM 33 CAA DRG 3 61.174 46.188 36.668 1.00 0.00
HETATM 34 CAB DRG 3 60.510 45.777 35.344 1.00 0.00
HETATM 35 CAC DRG 3 60.221 46.928 34.352 1.00 0.00
HETATM 36 CAD DRG 3 59.724 46.337 32.998 1.00 0.00
HETATM 37 CAE DRG 3 60.252 47.307 31.985 1.00 0.00
HETATM 38 CAF DRG 3 61.089 46.606 30.881 1.00 0.00
HETATM 39 CAG DRG 3 60.868 47.564 29.740 1.00 0.00
HETATM 40 CAH DRG 3 58.621 47.652 29.253 1.00 0.00
HETATM 41 CAI DRG 3 56.328 47.703 29.755 1.00 0.00
HETATM 42 CAJ DRG 3 55.914 48.516 30.963 1.00 0.00
HETATM 43 OAK DRG 3 55.050 49.545 30.403 1.00 0.00
HETATM 44 OAL DRG 3 54.945 47.724 31.565 1.00 0.00
HETATM 45 CAM DRG 3 54.420 47.478 29.367 1.00 0.00
HETATM 46 CAN DRG 3 53.587 47.142 27.983 1.00 0.00
HETATM 47 OAO DRG 3 52.713 48.009 27.325 1.00 0.00
HETATM 48 OAP DRG 3 53.396 45.805 27.517 1.00 0.00
HETATM 49 CAA DR1 4 50.257 46.173 36.646 1.00 0.00
HETATM 50 CAB DR1 4 49.673 45.778 35.270 1.00 0.00
HETATM 51 CAC DR1 4 49.360 46.939 34.273 1.00 0.00
HETATM 52 CAD DR1 4 49.270 46.480 32.735 1.00 0.00
HETATM 53 CAE DR1 4 50.289 47.086 31.602 1.00 0.00
HETATM 54 CAF DR1 4 51.813 46.713 31.234 1.00 0.00
HETATM 55 CAG DR1 4 52.487 47.720 29.966 1.00 0.00
HETATM 56 CAH DR1 4 50.870 47.989 29.178 1.00 0.00
HETATM 57 CAI DR1 4 48.982 47.816 29.191 1.00 0.00
HETATM 58 CAJ DR1 4 47.901 48.319 30.192 1.00 0.00
HETATM 59 OAK DR1 4 47.004 49.132 29.503 1.00 0.00
HETATM 60 OAL DR1 4 46.963 47.171 30.588 1.00 0.00
HETATM 61 CAM DR1 4 47.752 46.922 28.157 1.00 0.00
HETATM 62 CAN DR1 4 46.372 47.149 27.020 1.00 0.00
HETATM 63 OAO DR1 4 45.018 47.950 26.877 1.00 0.00
HETATM 64 OAP DR1 4 46.019 46.082 26.137 1.00 0.00
TER
ENDMDL


--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok,
but when I add one more repetitive unit (H-R-R-T) I get the following
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue. Can you
post the .pdb file?
-Justin
Post by nicegromacs
"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as well,
and identify the bond that is being formed that shouldn't.
-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://lists.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://lists.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
2009-08-14 18:46:19 UTC
Permalink
The problem is in how you handle impropers. From your previous post, your [DRG]
entry had the following:

[ impropers ]
CAG CAF -CAM C
-CAM -CAN -CAI C
CAJ CAI OAL O
CAN CAM OAP O
CAI CAH CAJ C

The last column needs to correspond to an actual atom name; there may also be
issues with atom naming, since that previous post also had different atom names
for DR0, DRG, and DR1 residues. In the attached .pdb file, you appear to have
uniform naming between all of the residues.

Be careful which files you are using; it looks like you have made multiple
attempts. If things still aren't working out, please post:

1. The error message you are getting.
2. The .pdb file.
3. The current .rtp entries.

-Justin
Post by nicegromacs
Hi Justin,
ups!! I am sorry this is the exact .pdb file.
HETATM 1 CAA DR0 1 83.043 46.127 36.820 1.00 0.00
HETATM 2 CAB DR0 1 82.411 45.765 35.421 1.00 0.00
HETATM 3 CAC DR0 1 81.495 46.822 34.598 1.00 0.00
HETATM 4 CAD DR0 1 80.621 46.369 33.071 1.00 0.00
HETATM 5 CAE DR0 1 79.305 47.302 32.172 1.00 0.00
HETATM 6 CAF DR0 1 77.939 46.749 31.124 1.00 0.00
HETATM 7 CAG DR0 1 76.264 47.439 30.612 1.00 0.00
HETATM 8 CAH DR0 1 74.636 46.805 29.962 1.00 0.00
HETATM 9 CAI DR0 1 72.805 47.674 30.179 1.00 0.00
HETATM 10 CAJ DR0 1 73.794 48.838 31.123 1.00 0.00
HETATM 11 OAK DR0 1 74.815 49.342 30.292 1.00 0.00
HETATM 12 OAL DR0 1 74.592 48.143 32.194 1.00 0.00
HETATM 13 CAM DR0 1 71.093 47.685 29.486 1.00 0.00
HETATM 14 CAN DR0 1 71.598 47.212 28.208 1.00 0.00
HETATM 15 OAO DR0 1 72.440 48.255 27.735 1.00 0.00
HETATM 16 OAP DR0 1 72.374 46.050 28.399 1.00 0.00
HETATM 17 CAA DRG 2 72.093 46.197 36.714 1.00 0.00
HETATM 18 CAB DRG 2 71.418 45.759 35.400 1.00 0.00
HETATM 19 CAC DRG 2 71.084 46.901 34.417 1.00 0.00
HETATM 20 CAD DRG 2 70.620 46.251 33.139 1.00 0.00
HETATM 21 CAE DRG 2 70.650 47.255 32.000 1.00 0.00
HETATM 22 CAF DRG 2 69.655 46.512 30.955 1.00 0.00
HETATM 23 CAG DRG 2 69.081 47.504 29.843 1.00 0.00
HETATM 24 CAH DRG 2 67.208 47.518 29.256 1.00 0.00
HETATM 25 CAI DRG 2 65.298 47.601 29.691 1.00 0.00
HETATM 26 CAJ DRG 2 65.629 48.362 30.827 1.00 0.00
HETATM 27 OAK DRG 2 65.140 49.590 30.429 1.00 0.00
HETATM 28 OAL DRG 2 64.837 47.815 31.709 1.00 0.00
HETATM 29 CAM DRG 2 63.041 47.557 29.333 1.00 0.00
HETATM 30 CAN DRG 2 62.808 47.023 27.931 1.00 0.00
HETATM 31 OAO DRG 2 63.130 48.142 27.185 1.00 0.00
HETATM 32 OAP DRG 2 63.560 45.894 27.706 1.00 0.00
HETATM 33 CAA DRG 3 61.174 46.188 36.668 1.00 0.00
HETATM 34 CAB DRG 3 60.510 45.777 35.344 1.00 0.00
HETATM 35 CAC DRG 3 60.221 46.928 34.352 1.00 0.00
HETATM 36 CAD DRG 3 59.724 46.337 32.998 1.00 0.00
HETATM 37 CAE DRG 3 60.252 47.307 31.985 1.00 0.00
HETATM 38 CAF DRG 3 61.089 46.606 30.881 1.00 0.00
HETATM 39 CAG DRG 3 60.868 47.564 29.740 1.00 0.00
HETATM 40 CAH DRG 3 58.621 47.652 29.253 1.00 0.00
HETATM 41 CAI DRG 3 56.328 47.703 29.755 1.00 0.00
HETATM 42 CAJ DRG 3 55.914 48.516 30.963 1.00 0.00
HETATM 43 OAK DRG 3 55.050 49.545 30.403 1.00 0.00
HETATM 44 OAL DRG 3 54.945 47.724 31.565 1.00 0.00
HETATM 45 CAM DRG 3 54.420 47.478 29.367 1.00 0.00
HETATM 46 CAN DRG 3 53.587 47.142 27.983 1.00 0.00
HETATM 47 OAO DRG 3 52.713 48.009 27.325 1.00 0.00
HETATM 48 OAP DRG 3 53.396 45.805 27.517 1.00 0.00
HETATM 49 CAA DR1 4 50.257 46.173 36.646 1.00 0.00
HETATM 50 CAB DR1 4 49.673 45.778 35.270 1.00 0.00
HETATM 51 CAC DR1 4 49.360 46.939 34.273 1.00 0.00
HETATM 52 CAD DR1 4 49.270 46.480 32.735 1.00 0.00
HETATM 53 CAE DR1 4 50.289 47.086 31.602 1.00 0.00
HETATM 54 CAF DR1 4 51.813 46.713 31.234 1.00 0.00
HETATM 55 CAG DR1 4 52.487 47.720 29.966 1.00 0.00
HETATM 56 CAH DR1 4 50.870 47.989 29.178 1.00 0.00
HETATM 57 CAI DR1 4 48.982 47.816 29.191 1.00 0.00
HETATM 58 CAJ DR1 4 47.901 48.319 30.192 1.00 0.00
HETATM 59 OAK DR1 4 47.004 49.132 29.503 1.00 0.00
HETATM 60 OAL DR1 4 46.963 47.171 30.588 1.00 0.00
HETATM 61 CAM DR1 4 47.752 46.922 28.157 1.00 0.00
HETATM 62 CAN DR1 4 46.372 47.149 27.020 1.00 0.00
HETATM 63 OAO DR1 4 45.018 47.950 26.877 1.00 0.00
HETATM 64 OAP DR1 4 46.019 46.082 26.137 1.00 0.00
TER
ENDMDL
--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
(I omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives
ok, but when I add one more repetitive unit (H-R-R-T) I get the
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue. Can
you post the .pdb file?
-Justin
Post by nicegromacs
"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at
least one terminus of your polymer chain. You may find this post
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as
well, and identify the bond that is being formed that shouldn't.
-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://lists.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://lists.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

========================================
nicegromacs
2009-08-14 19:05:32 UTC
Permalink
Hi Justin,
Ok, I have done some arrangements to the .rtp file (whit the same pdb file
DR0-DRG-DRG-DR1) but I still have the same error.

the rtp file is:
[ DRG ] ;
[ atoms ]
CAA CH3 0.000 1
CAB CH2 0.000 1
CAC CH2 0.000 1
CAD CH2 0.000 1
CAE CH2 0.000 2
CAF CH2 0.000 2
CAG CH1 0.000 3
CAH CH2 0.041 4
CAI CH1 0.107 4
CAJ C 0.352 4
OAK OM -0.750 4
OAL OM -0.750 4
CAM CH2 0.044 5
CAN C 0.373 5
OAO OM -0.709 5
OAP OM -0.708 5
[ bonds ]
CAM -CAG
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
CAG +CAM
[ impropers ]
CAG CAF -CAM CAH
-CAM -CAN -CAI CAG
CAJ CAI OAL OAK
CAN CAM OAP OAO
CAI CAH CAJ CAM

; head of the polymer

[ DR1 ]
[ atoms ]
CAA CH3 0.000 1
CAB CH2 0.000 1
CAC CH2 0.000 1
CAD CH2 0.000 1
CAE CH2 0.000 2
CAF CH2 0.000 2
CAG CH1 0.000 3
CAH CH2 0.041 4
CAI CH1 0.107 4
CAJ C 0.352 4
OAK OM -0.750 4
OAL OM -0.750 4
CAM CH2 0.044 5
CAN C 0.373 5
OAO OM -0.709 5
OAP OM -0.708 5
[ bonds ]
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
CAG +CAM
[ impropers ]
CAG CAF +CAM CAH
+CAM +CAN +CAI CAG
CAJ CAI OAL OAK
CAN CAM OAP OAO
CAI CAH CAJ CAM

; the tail of the polymer
[ DR2 ]
[ atoms ]
CAA CH3 0.000 1
CAB CH2 0.000 1
CAC CH2 0.000 1
CAD CH2 0.000 1
CAE CH2 0.000 2
CAF CH2 0.000 2
CAG CH1 0.000 3
CAH CH2 0.041 4
CAI CH1 0.107 4
CAJ C 0.352 4
OAK OM -0.750 4
OAL OM -0.750 4
CAM CH2 0.044 5
CAN C 0.373 5
OAO OM -0.709 5
OAP OM -0.708 5
[ bonds ]
CAM -CAG
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
[ impropers ]
CAG CAF -CAM CAH
-CAM -CAN -CAI CAG
CAJ CAI OAL OAK
CAN CAM OAP OAO
CAI CAH CAJ CAM

--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 2:46 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
The problem is in how you handle impropers. From your previous post, your
[ impropers ]
CAG CAF -CAM C
-CAM -CAN -CAI C
CAJ CAI OAL O
CAN CAM OAP O
CAI CAH CAJ C
The last column needs to correspond to an actual atom name; there may also
be issues with atom naming, since that previous post also had different
atom names for DR0, DRG, and DR1 residues. In the attached .pdb file, you
appear to have uniform naming between all of the residues.
Be careful which files you are using; it looks like you have made multiple
1. The error message you are getting.
2. The .pdb file.
3. The current .rtp entries.
-Justin
Post by nicegromacs
Hi Justin,
ups!! I am sorry this is the exact .pdb file.
HETATM 1 CAA DR0 1 83.043 46.127 36.820 1.00 0.00
HETATM 2 CAB DR0 1 82.411 45.765 35.421 1.00 0.00
HETATM 3 CAC DR0 1 81.495 46.822 34.598 1.00 0.00
HETATM 4 CAD DR0 1 80.621 46.369 33.071 1.00 0.00
HETATM 5 CAE DR0 1 79.305 47.302 32.172 1.00 0.00
HETATM 6 CAF DR0 1 77.939 46.749 31.124 1.00 0.00
HETATM 7 CAG DR0 1 76.264 47.439 30.612 1.00 0.00
HETATM 8 CAH DR0 1 74.636 46.805 29.962 1.00 0.00
HETATM 9 CAI DR0 1 72.805 47.674 30.179 1.00 0.00
HETATM 10 CAJ DR0 1 73.794 48.838 31.123 1.00 0.00
HETATM 11 OAK DR0 1 74.815 49.342 30.292 1.00 0.00
HETATM 12 OAL DR0 1 74.592 48.143 32.194 1.00 0.00
HETATM 13 CAM DR0 1 71.093 47.685 29.486 1.00 0.00
HETATM 14 CAN DR0 1 71.598 47.212 28.208 1.00 0.00
HETATM 15 OAO DR0 1 72.440 48.255 27.735 1.00 0.00
HETATM 16 OAP DR0 1 72.374 46.050 28.399 1.00 0.00
HETATM 17 CAA DRG 2 72.093 46.197 36.714 1.00 0.00
HETATM 18 CAB DRG 2 71.418 45.759 35.400 1.00 0.00
HETATM 19 CAC DRG 2 71.084 46.901 34.417 1.00 0.00
HETATM 20 CAD DRG 2 70.620 46.251 33.139 1.00 0.00
HETATM 21 CAE DRG 2 70.650 47.255 32.000 1.00 0.00
HETATM 22 CAF DRG 2 69.655 46.512 30.955 1.00 0.00
HETATM 23 CAG DRG 2 69.081 47.504 29.843 1.00 0.00
HETATM 24 CAH DRG 2 67.208 47.518 29.256 1.00 0.00
HETATM 25 CAI DRG 2 65.298 47.601 29.691 1.00 0.00
HETATM 26 CAJ DRG 2 65.629 48.362 30.827 1.00 0.00
HETATM 27 OAK DRG 2 65.140 49.590 30.429 1.00 0.00
HETATM 28 OAL DRG 2 64.837 47.815 31.709 1.00 0.00
HETATM 29 CAM DRG 2 63.041 47.557 29.333 1.00 0.00
HETATM 30 CAN DRG 2 62.808 47.023 27.931 1.00 0.00
HETATM 31 OAO DRG 2 63.130 48.142 27.185 1.00 0.00
HETATM 32 OAP DRG 2 63.560 45.894 27.706 1.00 0.00
HETATM 33 CAA DRG 3 61.174 46.188 36.668 1.00 0.00
HETATM 34 CAB DRG 3 60.510 45.777 35.344 1.00 0.00
HETATM 35 CAC DRG 3 60.221 46.928 34.352 1.00 0.00
HETATM 36 CAD DRG 3 59.724 46.337 32.998 1.00 0.00
HETATM 37 CAE DRG 3 60.252 47.307 31.985 1.00 0.00
HETATM 38 CAF DRG 3 61.089 46.606 30.881 1.00 0.00
HETATM 39 CAG DRG 3 60.868 47.564 29.740 1.00 0.00
HETATM 40 CAH DRG 3 58.621 47.652 29.253 1.00 0.00
HETATM 41 CAI DRG 3 56.328 47.703 29.755 1.00 0.00
HETATM 42 CAJ DRG 3 55.914 48.516 30.963 1.00 0.00
HETATM 43 OAK DRG 3 55.050 49.545 30.403 1.00 0.00
HETATM 44 OAL DRG 3 54.945 47.724 31.565 1.00 0.00
HETATM 45 CAM DRG 3 54.420 47.478 29.367 1.00 0.00
HETATM 46 CAN DRG 3 53.587 47.142 27.983 1.00 0.00
HETATM 47 OAO DRG 3 52.713 48.009 27.325 1.00 0.00
HETATM 48 OAP DRG 3 53.396 45.805 27.517 1.00 0.00
HETATM 49 CAA DR1 4 50.257 46.173 36.646 1.00 0.00
HETATM 50 CAB DR1 4 49.673 45.778 35.270 1.00 0.00
HETATM 51 CAC DR1 4 49.360 46.939 34.273 1.00 0.00
HETATM 52 CAD DR1 4 49.270 46.480 32.735 1.00 0.00
HETATM 53 CAE DR1 4 50.289 47.086 31.602 1.00 0.00
HETATM 54 CAF DR1 4 51.813 46.713 31.234 1.00 0.00
HETATM 55 CAG DR1 4 52.487 47.720 29.966 1.00 0.00
HETATM 56 CAH DR1 4 50.870 47.989 29.178 1.00 0.00
HETATM 57 CAI DR1 4 48.982 47.816 29.191 1.00 0.00
HETATM 58 CAJ DR1 4 47.901 48.319 30.192 1.00 0.00
HETATM 59 OAK DR1 4 47.004 49.132 29.503 1.00 0.00
HETATM 60 OAL DR1 4 46.963 47.171 30.588 1.00 0.00
HETATM 61 CAM DR1 4 47.752 46.922 28.157 1.00 0.00
HETATM 62 CAN DR1 4 46.372 47.149 27.020 1.00 0.00
HETATM 63 OAO DR1 4 45.018 47.950 26.877 1.00 0.00
HETATM 64 OAP DR1 4 46.019 46.082 26.137 1.00 0.00
TER
ENDMDL
--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives ok,
but when I add one more repetitive unit (H-R-R-T) I get the following
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue. Can
you post the .pdb file?
-Justin
Post by nicegromacs
"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at least
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as
well, and identify the bond that is being formed that shouldn't.
-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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--
========================================
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!
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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
========================================
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
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Justin A. Lemkul
2009-08-14 19:30:51 UTC
Permalink
Post by nicegromacs
Hi Justin,
Ok, I have done some arrangements to the .rtp file (whit the same pdb
file DR0-DRG-DRG-DR1) but I still have the same error.
Using these .rtp entries with the .pdb file you posted (after adjusting the
residue names) works for me, using version 4.0.5. Do you have problems with
other standard structures? It was weird that pdb2gmx was spitting out infinite
residue numbers. Does your installation pass the test set?

-Justin
Post by nicegromacs
[ DRG ] ;
[ atoms ]
CAA CH3 0.000 1
CAB CH2 0.000 1
CAC CH2 0.000 1
CAD CH2 0.000 1
CAE CH2 0.000 2
CAF CH2 0.000 2
CAG CH1 0.000 3
CAH CH2 0.041 4
CAI CH1 0.107 4
CAJ C 0.352 4
OAK OM -0.750 4
OAL OM -0.750 4
CAM CH2 0.044 5
CAN C 0.373 5
OAO OM -0.709 5
OAP OM -0.708 5
[ bonds ]
CAM -CAG
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
CAG +CAM
[ impropers ]
CAG CAF -CAM CAH
-CAM -CAN -CAI CAG
CAJ CAI OAL OAK
CAN CAM OAP OAO
CAI CAH CAJ CAM
; head of the polymer
[ DR1 ]
[ atoms ]
CAA CH3 0.000 1
CAB CH2 0.000 1
CAC CH2 0.000 1
CAD CH2 0.000 1
CAE CH2 0.000 2
CAF CH2 0.000 2
CAG CH1 0.000 3
CAH CH2 0.041 4
CAI CH1 0.107 4
CAJ C 0.352 4
OAK OM -0.750 4
OAL OM -0.750 4
CAM CH2 0.044 5
CAN C 0.373 5
OAO OM -0.709 5
OAP OM -0.708 5
[ bonds ]
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
CAG +CAM
[ impropers ]
CAG CAF +CAM CAH
+CAM +CAN +CAI CAG
CAJ CAI OAL OAK
CAN CAM OAP OAO
CAI CAH CAJ CAM
; the tail of the polymer
[ DR2 ]
[ atoms ]
CAA CH3 0.000 1
CAB CH2 0.000 1
CAC CH2 0.000 1
CAD CH2 0.000 1
CAE CH2 0.000 2
CAF CH2 0.000 2
CAG CH1 0.000 3
CAH CH2 0.041 4
CAI CH1 0.107 4
CAJ C 0.352 4
OAK OM -0.750 4
OAL OM -0.750 4
CAM CH2 0.044 5
CAN C 0.373 5
OAO OM -0.709 5
OAP OM -0.708 5
[ bonds ]
CAM -CAG
CAA CAB
CAB CAC
CAC CAD
CAD CAE
CAE CAF
CAF CAG
CAG CAH
CAH CAI
CAI CAJ
CAI CAM
CAJ OAK
CAJ OAL
CAM CAN
CAN OAO
CAN OAP
[ impropers ]
CAG CAF -CAM CAH
-CAM -CAN -CAI CAG
CAJ CAI OAL OAK
CAN CAM OAP OAO
CAI CAH CAJ CAM
--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 2:46 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
The problem is in how you handle impropers. From your previous post,
[ impropers ]
CAG CAF -CAM C
-CAM -CAN -CAI C
CAJ CAI OAL O
CAN CAM OAP O
CAI CAH CAJ C
The last column needs to correspond to an actual atom name; there may
also be issues with atom naming, since that previous post also had
different atom names for DR0, DRG, and DR1 residues. In the attached
.pdb file, you appear to have uniform naming between all of the residues.
Be careful which files you are using; it looks like you have made
1. The error message you are getting.
2. The .pdb file.
3. The current .rtp entries.
-Justin
Post by nicegromacs
Hi Justin,
ups!! I am sorry this is the exact .pdb file.
HETATM 1 CAA DR0 1 83.043 46.127 36.820 1.00 0.00
HETATM 2 CAB DR0 1 82.411 45.765 35.421 1.00 0.00
HETATM 3 CAC DR0 1 81.495 46.822 34.598 1.00 0.00
HETATM 4 CAD DR0 1 80.621 46.369 33.071 1.00 0.00
HETATM 5 CAE DR0 1 79.305 47.302 32.172 1.00 0.00
HETATM 6 CAF DR0 1 77.939 46.749 31.124 1.00 0.00
HETATM 7 CAG DR0 1 76.264 47.439 30.612 1.00 0.00
HETATM 8 CAH DR0 1 74.636 46.805 29.962 1.00 0.00
HETATM 9 CAI DR0 1 72.805 47.674 30.179 1.00 0.00
HETATM 10 CAJ DR0 1 73.794 48.838 31.123 1.00 0.00
HETATM 11 OAK DR0 1 74.815 49.342 30.292 1.00 0.00
HETATM 12 OAL DR0 1 74.592 48.143 32.194 1.00 0.00
HETATM 13 CAM DR0 1 71.093 47.685 29.486 1.00 0.00
HETATM 14 CAN DR0 1 71.598 47.212 28.208 1.00 0.00
HETATM 15 OAO DR0 1 72.440 48.255 27.735 1.00 0.00
HETATM 16 OAP DR0 1 72.374 46.050 28.399 1.00 0.00
HETATM 17 CAA DRG 2 72.093 46.197 36.714 1.00 0.00
HETATM 18 CAB DRG 2 71.418 45.759 35.400 1.00 0.00
HETATM 19 CAC DRG 2 71.084 46.901 34.417 1.00 0.00
HETATM 20 CAD DRG 2 70.620 46.251 33.139 1.00 0.00
HETATM 21 CAE DRG 2 70.650 47.255 32.000 1.00 0.00
HETATM 22 CAF DRG 2 69.655 46.512 30.955 1.00 0.00
HETATM 23 CAG DRG 2 69.081 47.504 29.843 1.00 0.00
HETATM 24 CAH DRG 2 67.208 47.518 29.256 1.00 0.00
HETATM 25 CAI DRG 2 65.298 47.601 29.691 1.00 0.00
HETATM 26 CAJ DRG 2 65.629 48.362 30.827 1.00 0.00
HETATM 27 OAK DRG 2 65.140 49.590 30.429 1.00 0.00
HETATM 28 OAL DRG 2 64.837 47.815 31.709 1.00 0.00
HETATM 29 CAM DRG 2 63.041 47.557 29.333 1.00 0.00
HETATM 30 CAN DRG 2 62.808 47.023 27.931 1.00 0.00
HETATM 31 OAO DRG 2 63.130 48.142 27.185 1.00 0.00
HETATM 32 OAP DRG 2 63.560 45.894 27.706 1.00 0.00
HETATM 33 CAA DRG 3 61.174 46.188 36.668 1.00 0.00
HETATM 34 CAB DRG 3 60.510 45.777 35.344 1.00 0.00
HETATM 35 CAC DRG 3 60.221 46.928 34.352 1.00 0.00
HETATM 36 CAD DRG 3 59.724 46.337 32.998 1.00 0.00
HETATM 37 CAE DRG 3 60.252 47.307 31.985 1.00 0.00
HETATM 38 CAF DRG 3 61.089 46.606 30.881 1.00 0.00
HETATM 39 CAG DRG 3 60.868 47.564 29.740 1.00 0.00
HETATM 40 CAH DRG 3 58.621 47.652 29.253 1.00 0.00
HETATM 41 CAI DRG 3 56.328 47.703 29.755 1.00 0.00
HETATM 42 CAJ DRG 3 55.914 48.516 30.963 1.00 0.00
HETATM 43 OAK DRG 3 55.050 49.545 30.403 1.00 0.00
HETATM 44 OAL DRG 3 54.945 47.724 31.565 1.00 0.00
HETATM 45 CAM DRG 3 54.420 47.478 29.367 1.00 0.00
HETATM 46 CAN DRG 3 53.587 47.142 27.983 1.00 0.00
HETATM 47 OAO DRG 3 52.713 48.009 27.325 1.00 0.00
HETATM 48 OAP DRG 3 53.396 45.805 27.517 1.00 0.00
HETATM 49 CAA DR1 4 50.257 46.173 36.646 1.00 0.00
HETATM 50 CAB DR1 4 49.673 45.778 35.270 1.00 0.00
HETATM 51 CAC DR1 4 49.360 46.939 34.273 1.00 0.00
HETATM 52 CAD DR1 4 49.270 46.480 32.735 1.00 0.00
HETATM 53 CAE DR1 4 50.289 47.086 31.602 1.00 0.00
HETATM 54 CAF DR1 4 51.813 46.713 31.234 1.00 0.00
HETATM 55 CAG DR1 4 52.487 47.720 29.966 1.00 0.00
HETATM 56 CAH DR1 4 50.870 47.989 29.178 1.00 0.00
HETATM 57 CAI DR1 4 48.982 47.816 29.191 1.00 0.00
HETATM 58 CAJ DR1 4 47.901 48.319 30.192 1.00 0.00
HETATM 59 OAK DR1 4 47.004 49.132 29.503 1.00 0.00
HETATM 60 OAL DR1 4 46.963 47.171 30.588 1.00 0.00
HETATM 61 CAM DR1 4 47.752 46.922 28.157 1.00 0.00
HETATM 62 CAN DR1 4 46.372 47.149 27.020 1.00 0.00
HETATM 63 OAO DR1 4 45.018 47.950 26.877 1.00 0.00
HETATM 64 OAP DR1 4 46.019 46.082 26.137 1.00 0.00
TER
ENDMDL
--------------------------------------------------
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Sent: Friday, August 14, 2009 12:14 PM
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] bad bond in polymer
Post by Justin A. Lemkul
Post by nicegromacs
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
(I omitted the change in the .hdb file because I don't have
explicit hydrogens). Well, I build a polymer with 3 units. The head
(H), one repeat unit (R)and tail (T) for the polymer (H-R-T) and
this gives ok, but when I add one more repetitive unit (H-R-R-T) I
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pgutil.c, line: 87
Atom CAM not found in residue 1083339441 while adding improper
-------------------------------------------------------
It looks like pdb2gmx is finding some kind of undefined residue.
Can you post the .pdb file?
-Justin
Post by nicegromacs
"Stop Drinking My Beer !" (The Amps)
Post by Justin A. Lemkul
Post by nicegromacs
CAG -CAM
Defining a bond to a previous residue will certainly fail for at
least one terminus of your polymer chain. You may find this post
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
If things still aren't working, please post the structure file, as
well, and identify the bond that is being formed that shouldn't.
-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://lists.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://lists.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://lists.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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