Tsjerk,
I just started to learn Gromacs. But how do I check the missing atoms?
Thanks,
Haining
On Wed, 10 Oct 2007 06:41:31 +0200 "Tsjerk Wassenaar" <[EMAIL PROTECTED] />wrote:
> 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, U!
niversity 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 fil!
e 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 Interac!
tive 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]m
issing 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 vo!
l 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 SG66
9 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 mail
ing list [email protected]
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
>
> --
> 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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