[gmx-users] pdb file error

Justin Lemkul jalemkul at vt.edu
Wed Aug 22 13:50:11 CEST 2012



On 8/22/12 7:44 AM, Sylwia Chmielewska wrote:
> Hello,
>
> I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I use to convert my file by PRODRG and MN.CONVERT.
> I'm trying to create a topology file from the pdb using the pdb2gmx. I get an error.
> My molecules are quaternary ammonium salts.
>
> My pdb file by MN. CONVERT:
> HEADER    NONE                                                          NONE   1
> TITLE                                                                   NONE   2
> AUTHOR    wwwrun                                                        NONE   3
> REVDAT   1  21-Aug-12     0                                             NONE   4
> ATOM      1  F           0       3.801   6.808   1.175  0.00  0.00           F+0
> ATOM      2  F           0       3.640   8.370  -0.485  0.00  0.00           F+0
> ATOM      3  F           0       4.526   8.939   1.521  0.00  0.00           F+0
> ATOM      4  F           0       5.676   7.548   0.128  0.00  0.00           F-1
> ATOM      5  B           0       4.423   7.922   0.589  0.00  0.00           B+0
> ATOM      6  O           0       0.490   7.739   3.751  0.00  0.00           O+0
> ATOM      7  N           0       1.215   6.101  -0.280  0.00  0.00           N+1
> ATOM      8  N           0       0.374   6.891   1.545  0.00  0.00           N+0
> ATOM      9  C           0       0.841   4.744  -3.562  0.00  0.00           C+0
> ATOM     10  H           0       1.512   4.109  -3.452  0.00  0.00           H+0
> ATOM     11  C           0      -1.173   6.617  -3.887  0.00  0.00           C+0
> ATOM     12  H           0      -1.849   7.246  -3.997  0.00  0.00           H+0
> ATOM     13  C           0       0.782   5.841  -2.713  0.00  0.00           C+0
> ATOM     14  C           0       1.819   6.022  -1.622  0.00  0.00           C+0
> ATOM     15  H           0       2.441   5.278  -1.649  0.00  0.00           H+0
> ATOM     16  C           0       0.899   5.023   0.522  0.00  0.00           C+0
> ATOM     17  H           0       1.021   4.125   0.314  0.00  0.00           H+0
> ATOM     18  C           0       0.886   7.217   0.359  0.00  0.00           C+0
> ATOM     19  H           0       0.996   8.081   0.035  0.00  0.00           H+0
> ATOM     20  C           0       2.645  11.347   7.810  0.00  0.00           C+0
> ATOM     21  H           0       2.215  10.478   7.846  0.00  0.00           H+0
> ATOM     22  C           0       2.640   7.702   4.776  0.00  0.00           C+0
> ATOM     23  H           0       2.632   6.757   4.560  0.00  0.00           H+0
> ATOM     24  C           0      -0.099   4.591  -4.572  0.00  0.00           C+0
> ATOM     25  H           0      -0.052   3.856  -5.141  0.00  0.00           H+0
> ATOM     26  C           0       4.137  11.172   8.131  0.00  0.00           C+0
> ATOM     27  H           0       4.569  12.039   8.082  0.00  0.00           H+0
> ATOM     28  C           0       1.772   8.442   3.770  0.00  0.00           C+0
> ATOM     29  H           0       2.185   8.369   2.884  0.00  0.00           H+0
> ATOM     30  C           0       1.541   9.918   4.083  0.00  0.00           C+0
> ATOM     31  H           0       1.014  10.306   3.368  0.00  0.00           H+0
> ATOM     32  C           0      -0.241   6.779  -2.874  0.00  0.00           C+0
> ATOM     33  H           0      -0.296   7.510  -2.302  0.00  0.00           H+0
> ATOM     34  C           0       4.388   8.760   7.296  0.00  0.00           C+0
> ATOM     35  H           0       3.419   8.760   7.343  0.00  0.00           H+0
> ATOM     36  C           0       4.099   8.190   4.815  0.00  0.00           C+0
> ATOM     37  H           0       4.586   7.782   4.083  0.00  0.00           H+0
> ATOM     38  C           0       4.871  10.204   7.197  0.00  0.00           C+0
> ATOM     39  H           0       4.761  10.508   6.282  0.00  0.00           H+0
> ATOM     40  C           0      -0.193   7.829   2.536  0.00  0.00           C+0
> ATOM     41  H           0      -0.131   8.736   2.196  0.00  0.00           H+0
> ATOM     42  C           0      -1.105   5.527  -4.738  0.00  0.00           C+0
> ATOM     43  H           0      -1.731   5.424  -5.417  0.00  0.00           H+0
> ATOM     44  C           0       0.381   5.518   1.660  0.00  0.00           C+0
> ATOM     45  H           0       0.083   5.026   2.389  0.00  0.00           H+0
> ATOM     46  C           0       2.362  11.979   6.442  0.00  0.00           C+0
> ATOM     47  H           0       2.450  12.942   6.518  0.00  0.00           H+0
> ATOM     48  C           0       4.822   7.868   6.127  0.00  0.00           C+0
> ATOM     49  H           0       5.777   7.969   5.993  0.00  0.00           H+0
> ATOM     50  C           0       0.834  10.200   5.414  0.00  0.00           C+0
> ATOM     51  H           0       1.200   9.612   6.094  0.00  0.00           H+0
> ATOM     52  C           0       0.970  11.651   5.890  0.00  0.00           C+0
> ATOM     53  H           0       0.779  12.245   5.147  0.00  0.00           H+0
> CONECT    1    5    0    0    0                                         NONE  58
> CONECT    2    5    0    0    0                                         NONE  59
> CONECT    3    5    0    0    0                                         NONE  60
> CONECT    5    1    2    3    0                                         NONE  61
> CONECT    6   40   28    0    0                                         NONE  62
> CONECT    7   18   16   14    0                                         NONE  63
> CONECT    8   18   44   40    0                                         NONE  64
> CONECT    9   10   13   24    0                                         NONE  65
> CONECT   11   12   42   32    0                                         NONE  66
> CONECT   13    9   32   14    0                                         NONE  67
> CONECT   14    7   13   15    0                                         NONE  68
> CONECT   16    7   17   44    0                                         NONE  69
> CONECT   18    7    8   19    0                                         NONE  70
> CONECT   20   21   46   26    0                                         NONE  71
> CONECT   22   23   28   36    0                                         NONE  72
> CONECT   24    9   25   42    0                                         NONE  73
> CONECT   26   20   27   38    0                                         NONE  74
> CONECT   28    6   22   29   30                                         NONE  75
> CONECT   30   28   31   50    0                                         NONE  76
> CONECT   32   11   13   33    0                                         NONE  77
> CONECT   34   35   38   48    0                                         NONE  78
> CONECT   36   22   37   48    0                                         NONE  79
> CONECT   38   26   34   39    0                                         NONE  80
> CONECT   40    6    8   41    0                                         NONE  81
> CONECT   42   11   24   43    0                                         NONE  82
> CONECT   44    8   16   45    0                                         NONE  83
> CONECT   46   20   47   52    0                                         NONE  84
> CONECT   48   34   36   49    0                                         NONE  85
> CONECT   50   30   51   52    0                                         NONE  86
> CONECT   52   46   50   53    0                                         NONE  87
> END
>
> I choose Gromos 53a6 with none the water model, then appear an error:
>
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
> Reading bf4.pdb...
> WARNING: all CONECT records are ignored
> Read 'NONE   2', 53 atoms
> Analyzing pdb file
> Splitting PDB chains based on TER records or changing chain id.
> There are 1 chains and 0 blocks of water and 0 residues with 53 atoms
>
>    chain  #res #atoms
>    1 ' '     1     53
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp
> Atomtype 1
> Reading residue database... (gromos53a6)
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing impropers on same bond as a proper
> Residue 108
> Sorting it all out...
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
> Opening force field file /usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
> Processing chain 1 (53 atoms, 1 residues)
> There are 2 donors and 1 acceptors
> There are 1 hydrogen bonds
> Warning: Starting residue 0 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 4.5.3
> Source code file: /build/buildd/gromacs-4.5.3/src/kernel/resall.c, line: 581
>
> Fatal error:
> Residue '' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> With the PRODGR is very similary:
> The pdb file look:
>
> HETATM    1  CAR DRG     1       8.910   1.560  -1.040  1.00 20.00             C
> HETATM    2  CAP DRG     1       9.300   0.100  -1.220  1.00 20.00             C
> HETATM    3  CAN DRG     1       9.860  -0.130  -2.620  1.00 20.00             C
> HETATM    4  CAL DRG     1      10.720  -1.390  -2.690  1.00 20.00             C
> HETATM    5  CAJ DRG     1      12.130  -1.170  -2.140  1.00 20.00             C
> HETATM    6  CAI DRG     1      12.170  -1.220  -0.620  1.00 20.00             C
> HETATM    7  CAK DRG     1      13.410  -0.520  -0.090  1.00 20.00             C
> ...
>
> Fatal error:
> Residue 'DRG' not found in residue topology database
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I check Documentation/Errors. It not found 'XXX' in residue topology database.
> Then I use command x2top and appear: x2top: command not found
>

The command is g_x2top.

> Will you please tell me what sholud I do to solve the problem?
>
> Where could I find residue 'XXX' to my compound?
>

'XXX' is a generic indicator signifying some residue name.  The content of that 
error description should tell you what you need to know - pdb2gmx isn't magic, 
and if you want it to create a topology, you need an .rtp entry for every 
residue that appears in your .pdb file.  If you used PRODRG, it should give you 
a topology.  That topology will likely have significant defects and will require 
manual modification, but it's at least a start.

> I read about force field in gromacs website http://www.gromacs.org/Documentation/Terminology/Force_Fields
> What kind of force field should I use to my compounds?
> I choose gromos 53a6, but I don't know if it fits.
>

You should not choose a force field haphazardly.  Spending significant time in 
the literature reading about the various force fields and how they have been 
used would be wise.  What have other investigators done with systems similar to 
yours?  A few hours spent reading will save you weeks of wasted time if you find 
out your force field choice was unsuitable.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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