[gmx-users] ionomer topolgy
Ehsan Sadeghi
esa38 at sfu.ca
Fri Sep 27 21:17:50 CEST 2013
Many thanks Justin.
Here is my .pdb file:
ATOM 1 C LIG 1 -10.450 5.214 -1.717 1.00 0.00 C
ATOM 2 C LIG 1 -8.424 5.477 -1.030 1.00 0.00 C
ATOM 3 C LIG 1 -6.603 5.864 -0.166 1.00 0.00 C
ATOM 4 F LIG 1 -6.651 6.230 -1.691 1.00 0.00 F
ATOM 5 F LIG 1 -8.417 4.546 -2.349 1.00 0.00 F
ATOM 6 C LIG 1 -5.705 3.003 1.204 1.00 0.00 C
ATOM 7 F LIG 1 -7.247 5.032 1.683 1.00 0.00 F
ATOM 8 F LIG 1 -8.521 5.307 0.400 1.00 0.00 F
ATOM 9 C LIG 1 -3.913 4.878 2.109 1.00 0.00 C
ATOM 10 F LIG 1 -4.358 3.650 -0.024 1.00 0.00 F
ATOM 11 F LIG 1 -6.198 1.346 0.214 1.00 0.00 F
ATOM 12 C LIG 1 -1.306 5.673 2.286 1.00 0.00 C
ATOM 13 F LIG 1 -3.429 3.111 0.668 1.00 0.00 F
ATOM 14 F LIG 1 -2.358 3.855 1.570 1.00 0.00 F
ATOM 15 C LIG 1 0.246 3.040 2.048 1.00 0.00 C
ATOM 16 F LIG 1 -0.514 4.358 3.241 1.00 0.00 F
ATOM 17 F LIG 1 -0.928 3.807 1.741 1.00 0.00 F
ATOM 18 C LIG 1 1.925 3.706 2.014 1.00 0.00 C
ATOM 19 F LIG 1 -0.226 2.548 0.094 1.00 0.00 F
ATOM 20 F LIG 1 0.215 1.482 1.590 1.00 0.00 F
ATOM 21 F LIG 1 -11.789 4.355 -2.598 1.00 0.00 F
ATOM 22 F LIG 1 -11.552 4.133 -0.632 1.00 0.00 F
ATOM 23 F LIG 1 2.299 2.385 2.438 1.00 0.00 F
ATOM 24 F LIG 1 1.831 1.994 1.526 1.00 0.00 F
ATOM 25 OM SCH 2 3.334 3.720 1.360 1.00 0.00 O
ATOM 26 C SCH 2 5.273 2.985 0.897 1.00 0.00 C
ATOM 27 C SCH 2 6.100 2.445 1.642 1.00 0.00 C
ATOM 28 F SCH 2 4.528 2.997 1.631 1.00 0.00 F
ATOM 29 F SCH 2 6.122 3.473 0.467 1.00 0.00 F
ATOM 30 C SCH 2 7.274 1.746 2.026 1.00 0.00 C
ATOM 31 OM SCH 2 5.454 2.160 2.446 1.00 0.00 O
ATOM 32 F SCH 2 6.788 2.944 0.993 1.00 0.00 F
ATOM 33 F SCH 2 7.031 1.025 2.779 1.00 0.00 F
ATOM 34 F SCH 2 8.010 2.431 2.393 1.00 0.00 F
ATOM 35 F SCH 2 7.678 1.241 1.173 1.00 0.00 F
ATOM 36 C SCH 2 5.042 1.305 2.243 1.00 0.00 C
ATOM 37 C SCH 2 5.168 0.043 2.583 1.00 0.00 C
ATOM 38 F SCH 2 4.938 1.296 1.178 1.00 0.00 F
ATOM 39 F SCH 2 4.377 1.446 3.070 1.00 0.00 F
ATOM 40 S SCH 2 5.516 -1.463 2.733 1.00 0.00 S
ATOM 41 F SCH 2 4.304 0.015 3.213 1.00 0.00 F
ATOM 42 F SCH 2 6.073 0.088 2.014 1.00 0.00 F
ATOM 43 O SCH 2 4.555 -2.079 3.473 1.00 0.00 O
ATOM 44 H SCH 2 4.772 -3.020 3.567 1.00 0.00 H
ATOM 45 O SCH 2 6.692 -1.508 1.977 1.00 0.00 O
ATOM 46 O SCH 2 6.001 -2.846 2.762 1.00 0.00 O
CONECT 1 2 21 22
CONECT 2 1 3 4 5
CONECT 2
CONECT 3 2 6 7 8
CONECT 3
CONECT 4 2
CONECT 5 2
CONECT 6 3 9 10 11
CONECT 6
CONECT 7 3
CONECT 8 3
CONECT 9 6 12 13 14
CONECT 9
CONECT 10 6
CONECT 11 6
CONECT 12 9 15 16 17
CONECT 12
CONECT 13 9
CONECT 14 9
CONECT 15 12 18 19 20
CONECT 15
CONECT 16 12
CONECT 17 12
CONECT 18 15 23 24 25
CONECT 18
CONECT 19 15
CONECT 20 15
CONECT 21 1
CONECT 22 1
CONECT 23 18
CONECT 24 18
CONECT 25 18 26
CONECT 26 25 27 28 29
CONECT 26
CONECT 27 26 30 31 32
CONECT 27
CONECT 28 26
CONECT 29 26
CONECT 30 27 33 34 35
CONECT 30
CONECT 31 27 36
CONECT 32 27
CONECT 33 30
CONECT 34 30
CONECT 35 30
CONECT 36 31 37 38 39
CONECT 36
CONECT 37 36 40 41 42
CONECT 37
CONECT 38 36
CONECT 39 36
CONECT 40 37 43 45 46
CONECT 40
CONECT 41 37
CONECT 42 37
CONECT 43 40 44
CONECT 44 43
CONECT 45 40
CONECT 46 40
MASTER 0 0 0 0 0 0 0 0 46 0 46 0
END
-------------------------------------------------
I already added LIG and SCH in residuetypes.dat and defined the atoms for each residue in aminoacids.rtp in gromos. When I run pdb2gmx -f nafion.pdb
I receive this error:
Warning: Starting residue LIG1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue SCH2 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
-------------------------------------------------------
Program pdb2gmx, VERSION 4.6.3
Source code file: /home/ehssad/Downloads/Gromacs/gromacs-4.6.3/src/kernel/resall.c, line: 642
Fatal error:
Residue 'LIG' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
Thank you,
Ehsan
----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Friday, September 27, 2013 11:50:13 AM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 2:34 PM, Ehsan Sadeghi wrote:
> Hello Gromacs users,
>
> I am the beginner in Gromacs. I want to simulate ionomer in water. I could
> not find a pdb file for my case, and I tried to draw the ionomer in Avogadro
> software and generated the pdb file. However, gmx cannot find my residue
> names. I added my residue name to residuetypes.dat and added the residue in
> aminoacids.rtp in gromos. I does not work and it cannot find my new residue.
> What should I do?
>
Well, there are several Gromos parameter sets; have you modified and then chosen
the correct one? In the absence of more detail, it's hard to figure out what's
gone wrong.
> I also have some question regarding the .rtp file. Do you I need to include [
> bonds] , [angles], [dihedrals] as well? How can I find charge and charge
> groups in the [ atoms] section.
>
You need to at least specify [bonds], from which the angles and dihedrals can be
generated. If you have planar groups, you need to specify [impropers] for them.
Parametrization methods vary by force field, but if you're using a Gromos
parameter set, most of the functional groups should be easily transferable to
new species. If you are dealing with something totally new, then you need to
derive the charges yourself. Details should be available in the primary
literature for whatever parameter set you've chosen, as well as publications by
others. Prepare to invest some time here; it's not necessarily trivial to
derive the new values.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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