[gmx-users] pdb2gmx stop at "AtomType 1"(Justin)
Justin A. Lemkul
jalemkul at vt.edu
Sun Oct 17 01:28:05 CEST 2010
英雄不再寂寞 wrote:
> Date: Sat, 16 Oct 2010 08:36:00 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] pdb2gmx stop at "AtomType 1"
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CB99C30.50105 at vt.edu>
> Content-Type: text/plain; charset=x-gbk; format=flowed
> 英雄不再寂寞 wrote:
> > 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.
>
> Q: Did you also add an entry in residuetypes.dat and aminoacids.hdb (if
> necessary)?
>
> -Justin
>
> A: Yes, I added the entry in residuetypes.dat like:
> DET Organic
>
To what does "Organic" refer? Is that even a recognized keyword? What is the
nature of the residue you've added? Does adding "-debug 1" to your pdb2gmx
command line provide any useful information in the resulting .log file?
-Justin
> > Chaofu Wu, Dr.
> >
> > xiaowu759 at linux-s38y:~/workshop
> > <mailto: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
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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