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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