[gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens

Wed Oct 10 07:21:20 CEST 2007

Hi Haining,

This has nothing to do with gromacs. The information is in the .pdb file
(use a text viewer/editor). Before starting any simulation, you have to know
what you're intending to simulate. The model, the .pdb file of it. How the
structure was solved, etc., etc. The paper should also state which parts of
the molecule were not (well) resolved. In case you have missing atoms and
residues, you have to find a way to deal with that (model them in, for
example).

Did you run the tutorials mentioned on the Gromacs site?

Tsjerk

On 10/10/07, Haining Liu <liu123s at uwindsor.ca> wrote:
>
> 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" wrote:
> > Haining,
> >
> > Did you check the structure for missing atoms/residues (REMARK 465/470)?
>
> >
> > Tsjerk
> >
> > On 10/10/07, Haining Liu 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 gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before
> posting!
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> > > 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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>

-- 
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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