Thanks. Sylwia ----- Oryginalna wiadomość ----- Od: "Justin Lemkul" <jalem...@vt.edu> Do: "Discussion list for GROMACS users" <gmx-users@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" <jalem...@vt.edu> > Do: "Discussion list for GROMACS users" <gmx-users@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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