[gmx-users] pdb file error
Sylwia Chmielewska
sylwia.t.chmielewska at doctorate.put.poznan.pl
Wed Aug 22 13:44:53 CEST 2012
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
Will you please tell me what sholud I do to solve the problem?
Where could I find residue 'XXX' to my compound?
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.
Thanks for your suggestions.
Best Reagrds
Sylwia
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