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" <jalem...@vt.edu>
To: "Discussion list for GROMACS users" <gmx-users@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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