[gmx-users] ionomer topolgy
Ehsan Sadeghi
esa38 at sfu.ca
Fri Sep 27 22:18:20 CEST 2013
Hi,
I just added this to the existing .rtp file in gromos
[ LIG ]
[ atoms ]
C C 0.000 0
F F 0.000 0
[ SCH ]
[ atoms ]
O OM 0.000 0
C C 0.000 0
O O 0.000 0
F F 0.000 0
S S 0.000 0
H H 0.000 0
I also added LIG and SCH to the residuetypes.dat
Kind regards,
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 12:29:38 PM
Subject: Re: [gmx-users] ionomer topolgy
On 9/27/13 3:17 PM, Ehsan Sadeghi wrote:
> 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
>
You still haven't provided any real useful diagnostic information. What do the
.rtp entries look like? Which force field did you modify? Did you modify a
local copy of it, or the one in $GMXLIB? Based on that, are you making the
right choice when running pdb2gmx?
-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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