Haining,<br><br>Did you check the structure for missing atoms/residues (REMARK 465/470)?<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 10/10/07, <b class="gmail_sendername">Haining Liu</b> <<a href="mailto:liu123s@uwindsor.ca">
liu123s@uwindsor.ca</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>I have a problem using Gromacs. When I use the pdb2gmx command to
<br>generate the .top and .gro files, I got the error:<br><br> :-) G R O M A C S (-:<br><br> Gyas ROwers Mature At Cryogenic Speed<br><br> :-) VERSION
3.3.2 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and<br>others.<br> Copyright (c) 1991-2000, University of Groningen, The<br>Netherlands.<br> Copyright (c) 2001-2007, The GROMACS development team,
<br> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br><br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License
<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br> :-) pdb2gmx (-:<br><br>Option Filename Type Description
<br>------------------------------------------------------------<br> -f 2FDG.pdb Input Generic structure: gro g96 pdb tpr<br>tpb tpa<br> xml<br> -o 2FDG.gro Output Generic structure: gro g96 pdb xml
<br> -p 2FDG.top Output Topology file<br> -i posre.itp Output Include file for topology<br> -n clean.ndx Output, Opt. Index file<br> -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml
<br><br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-[no]X bool no Use dialog box GUI to edit command line
<br>options<br>-nice int 0 Set the nicelevel<br>-[no]merge bool no Merge chains into one molecule definition<br>-ff string select Force field, interactive by default. Use -<br>h for<br> information.
<br>-water enum spc Water model to use: with GROMOS we<br>recommend SPC,<br> with OPLS, TIP4P: spc, spce, tip3p,<br>tip4p, tip5p<br> or f3c<br>-[no]inter bool no Set the next 6 options to interactive
<br>-[no]ss bool no Interactive SS bridge selection<br>-[no]ter bool no Interactive termini selection, iso charged<br>-[no]lys bool no Interactive Lysine selection, iso charged<br>-[no]arg bool no Interactive Arganine selection, iso charged
<br>-[no]asp bool no Interactive Aspartic Acid selection, iso<br>charged<br>-[no]glu bool no Interactive Glutamic Acid selection, iso<br>charged<br>-[no]gln bool no Interactive Glutamine selection, iso neutral
<br>-[no]his bool no Interactive Histidine selection, iso<br>checking<br> H-bonds<br>-angle real 135 Minimum hydrogen-donor-acceptor angle for a<br> H-bond (degrees)
<br>-dist real 0.3 Maximum donor-acceptor distance for a H-<br>bond (nm)<br>-[no]una bool no Select aromatic rings with united CH<br>atoms on<br> Phenylalanine, Tryptophane and Tyrosine
<br>-[no]ignh bool no Ignore hydrogen atoms that are in the pdb<br>file<br>-[no]missing bool no Continue when atoms are missing, dangerous<br>-[no]v bool no Be slightly more verbose in messages
<br>-posrefc real 1000 Force constant for position restraints<br>-vsite enum none Convert atoms to virtual sites: none,<br>hydrogens<br> or aromatics<br>-[no]heavyh bool no Make hydrogen atoms heavy
<br>-[no]deuterate bool no Change the mass of hydrogens to 2 amu<br><br>Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat<br><br>Select the Force Field:<br>0: GROMOS96 43a1 force field<br>1: GROMOS96 43b1 vacuum force field
<br>2: GROMOS96 43a2 force field (improved alkane dihedrals)<br>3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
<br>6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>7: Encad all-atom force field, using scaled-down vacuum charges<br>8: Encad all-atom force field, using full solvent charges<br>0<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp
<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>Reading 2FDG.pdb...<br>WARNING: all CONECT records are ignored<br>Read 'ALKYLATED DNA REPAIR PROTEIN ALKB; 5'-D(P*TP*(MA7)P*T)-3'',
<br>1747 atoms<br>Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat<br>26 out of 26 lines of xlateat.dat converted succesfully<br>Analyzing pdb file<br>Gave chain 3 chain identifier 'C'<br>There are 3 chains and 1 blocks of water and 324 residues with 1747
<br>atoms<br><br> chain #res #atoms<br> 1 'A' 200 1556<br> 2 'B' 3 63<br> 3 'C' 2 9<br> 4 '-' 119 119 (only water)<br><br>All occupancies are one<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.atp
<br>Atomtype 50<br>Reading residue database... (ffG43a1)<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.rtp<br>Residue 96<br>Sorting it all out...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.hdb
<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1-n.tdb<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1-c.tdb<br>Processing chain 1 'A' (1556 atoms, 200 residues)<br>There are 307 donors and 274 acceptors
<br>There are 442 hydrogen bonds<br>Will use HISB for residue 52<br>Will use HISB for residue 58<br>Will use HISB for residue 83<br>Will use HISA for residue 117<br>Will use HISB for residue 158<br>Will use HISA for residue 173
<br>Will use HISB for residue 183<br>Checking for duplicate atoms....<br>Opening library file /usr/local/gromacs/share/gromacs/top/specbond.dat<br>6 out of 6 lines of specbond.dat converted succesfully<br>Special Atom Distance matrix:
<br> MET35 MET43 MET47 CYS50 HISB52 HISB58<br>MET78<br> SD270 SD326 SD352 SG374 NE2388 NE2438<br>SD603<br> MET43 SD326 0.512<br> MET47 SD352 0.404 0.438
<br> CYS50 SG374 1.375 1.733 1.304<br> HISB52 NE2388 1.976 2.415 2.060 1.098<br> HISB58 NE2438 1.169 1.333 1.453 2.160 2.198<br> MET78 SD603 1.727 2.055 1.634 0.534 0.889
2.316<br> HISB83 NE2647 2.030 2.379 1.967 0.828 0.738 2.511<br>0.354<br> CYS86 SG669 1.983 2.179 1.783 1.042 1.412 2.546<br>0.647<br> CYS103 SG793 1.332 1.583 1.151 0.441 1.336
2.130<br>0.571<br>HISA117 NE2902 1.137 0.874 0.844 1.778 2.418 1.659 1.898<br>HISB158 NE21226 2.370 2.389 2.050 1.701 2.709 3.430 1.866<br>HISA173 NE21348 1.409 1.201 1.096 1.797
2.415 1.898 1.833<br>HISB183 NE21423 2.480 2.432 2.147 2.005 3.052 3.576 2.217<br> CYS189 SG1467 1.697 1.684 1.437 1.597 2.689 2.859<br>2.005<br> HISB83 CYS86 CYS103 HISA117 HISB158 HISA173
<br>HISB183<br> NE2647 SG669 SG793 NE2902 NE21226 NE21348<br>NE21423<br> CYS86 SG669 0.777<br> CYS103 SG793 0.924 0.768<br>HISA117 NE2902 2.208 1.758 1.443<br>HISB158 NE21226
2.113 1.745 1.523 2.213<br>HISA173 NE21348 2.125 1.581 1.410 0.343 2.126<br>HISB183 NE21423 2.484 2.093 1.818 2.292 0.403 2.228<br> CYS189 SG1467 2.327 2.111 1.513 1.882 1.060 1.967
<br>0.992<br><br><br>N-terminus: NH3+<br>C-terminus: COO-<br>WARNING: atom CA not found in residue 200 while adding atom<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.2<br>
Source code file: genhydro.c, line: 304<br><br>Fatal error:<br>Atom CA not found in residue LYSH200 while adding hydrogens<br>-------------------------------------------------------<br><br>"She's a Good Sheila Bruce" (Monty Python)
<br><br>The pdb file is downloaded from <a href="http://www.pdb.org">www.pdb.org</a> without any changing. Can<br>someone help to fix this problem?<br><br>Thanks,<br>Haining<br>_______________________________________________
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Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931 <br>F: +31-30-2537623