> Chaofu Wu, Dr.
>
> xiaowu...@linux-s38y:~/workshop
> <mailto:xiaowu...@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
