[gmx-users] pdb2gmx stop at "AtomType 1"
英雄不再寂寞
xiaowu759 at qq.com
Sat Oct 16 12:38:49 CEST 2010
Dear gmx-users,
I have added the required residue groups in the rtp file. Then I run the pdb2gmx using the following line for the top file, only to stop at " AtomType 1". No any message is given. I can not think out what is happening at all. Please help me with this problem, thanks a lot. Note that I am using gmx-4.5.
Chaofu Wu, Dr.
xiaowu759 at linux-s38y:~/workshop> pdb2gmx -f deta.pdb -o deta.gro -p deta.top -i deta.itp -ter
:-) G R O M A C S (-:
Gromacs Runs One Microsecond At Cannonball Speeds
:-) VERSION 4.5.1 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, P盲r Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
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 deta.pdb Input Structure file: gro g96 pdb tpr etc.
-o deta.gro Output Structure file: gro g96 pdb etc.
-p deta.top Output Topology file
-i deta.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-chainsep enum id_or_ter Condition in PDB files when a new chain and
molecule_type should be started: id_or_ter,
id_and_ter, ter, id or interactive
-ff string select Force field, interactive by default. Use -h for
information.
-water enum select Water model to use: select, none, spc, spce,
tip3p, tip4p or tip5p
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool yes 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
-[no]chargegrp bool yes Use charge groups in the rtp file
-[no]cmap bool yes Use cmap torsions (if enabled in the rtp file)
-[no]renum bool no Renumber the residues consecutively in the output
-[no]rtpres bool no Use rtp entry names as residue names
Select the Force Field:
From current directory:
1: CNT_OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
2: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
From '/usr/local/gromacs/share/gromacs/top':
3: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
4: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
5: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
6: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
7: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
8: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
9: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
10: CHARMM27 all-atom force field (with CMAP) - version 2.0beta
11: GROMOS96 43a1 force field
12: GROMOS96 43a2 force field (improved alkane dihedrals)
13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
17: [DEPRECATED] Encad all-atom force field, using full solvent charges
18: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
19: [DEPRECATED] Gromacs force field (see manual)
20: [DEPRECATED] Gromacs force field with hydrogens for NMR
16
Using the Oplsaa force field in directory oplsaa.ff
Opening force field file oplsaa.ff/watermodels.dat
Select the Water Model:
1: TIP4P TIP 4-point, recommended
2: TIP3P TIP 3-point
3: TIP5P TIP 5-point
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
6
Opening force field file oplsaa.ff/aminoacids.r2b
Reading deta.pdb...
Read 20 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 1 residues with 20 atoms
chain #res #atoms
1 ' ' 1 20
All occupancies are one
Opening force field file oplsaa.ff/atomtypes.atp
Atomtype 1
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