[gmx-users] pdb file error

Sylwia Chmielewska sylwia.t.chmielewska at doctorate.put.poznan.pl
Wed Aug 22 15:07:48 CEST 2012


Thanks.
Sylwia

----- Oryginalna wiadomość -----
Od: "Justin Lemkul" <jalemkul at vt.edu>
Do: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Wysłane: środa, 22 sierpień 2012 14:56:16
Temat: Re: [gmx-users] pdb file error



On 8/22/12 8:48 AM, Sylwia Chmielewska wrote:
> Thank you for your prompt reply. I will take to read about force field.
> Could you recommend websites for field force? Or other information about force field.
>

You can find primary literature for the various force fields available in 
Gromacs within the manual.  Beyond that, even Google searching will turn up 
useful results within seconds.

-Justin

> Best Regards
> Sylwia
> ----- Oryginalna wiadomość -----
> Od: "Justin Lemkul" <jalemkul at vt.edu>
> Do: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Wysłane: środa, 22 sierpień 2012 13:50:11
> Temat: Re: [gmx-users] pdb file error
>
>
>
> 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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