<p>Tsjerk,</p><p>I just started to learn Gromacs. But how do I check the missing atoms?</p><p>Thanks,</p><p>Haining</p><p>On Wed, 10 Oct 2007 06:41:31 +0200 "Tsjerk Wassenaar" <tsjerkw@gmail.com />wrote: <br />> Haining, <br />> <br />> Did you check the structure for missing atoms/residues (REMARK 465/470)? <br />> <br />> Tsjerk <br />> <br />> On 10/10/07, Haining Liu <liu123s@uwindsor.ca />wrote: <br />> > <br />> > 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, U!
niversity of Groningen, The <br />> > Netherlands. <br />> > Copyright (c) 2001-2007, The GROMACS development team, <br />> > check out http://www.gromacs.org 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 fil!
e for topology <br />> > -n clean.ndx Output, Opt. Index file <b
r />> > -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 Interac!
tive 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]m
issing 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 vo!
l 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 SG66
9 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 www.pdb.org without any changing. Can <br />> > someone help to fix this problem? <br />> > <br />> > Thanks, <br />> > Haining <br />> > ________!
_______________________________________ <br />> > gmx-users mail
ing list gmx-users@gromacs.org <br />> > http://www.gromacs.org/mailman/listinfo/gmx-users <br />> > Please search the archive at http://www.gromacs.org/search before posting! <br />> > Please don't post (un)subscribe requests to the list. Use the <br />> > www interface or send it to gmx-users-request@gromacs.org. <br />> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php <br />> > <br />> <br />> <br />> <br />> -- <br />> Tsjerk A. Wassenaar, 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 </p>