[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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