[gmx-users] Fatal error: Atom CA not found in residue LYSH200 while adding hydrogens
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Oct 10 06:41:31 CEST 2007
Haining,
Did you check the structure for missing atoms/residues (REMARK 465/470)?
Tsjerk
On 10/10/07, Haining Liu <liu123s at uwindsor.ca> 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
> _______________________________________________
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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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