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