[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
========================================
More information about the gromacs.org_gmx-users
mailing list