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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