<DIV><includetail>Date: Sat, 16 Oct 2010 08:36:00 -0400<BR>From: "Justin A. Lemkul" <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] pdb2gmx stop at "AtomType 1"<BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>Message-ID: <4CB99C30.50105@vt.edu><BR>Content-Type: text/plain; charset=x-gbk; format=flowed<BR>Ó¢ÐÛ²»ÔÙ¼Åį wrote:<BR>> Dear gmx-users,<BR>> I have added the required residue groups in the rtp file. Then I run <BR>> the pdb2gmx using the following line for the top file, only to stop at " <BR>> AtomType 1". No any message is given. I can not think out what is <BR>> happening at all. Please help me with this problem, thanks a lot. Note <BR>> that I am using gmx-4.5.<BR><BR>Q: Did you also add an entry in residuetypes.dat and aminoacids.hdb (if necessary)?<BR><BR>-Justin</includetail></DIV>
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<DIV>A: Yes, I added the entry in residuetypes.dat like:</:includetail></DIV>
<DIV>DET Organic<BR><BR>> Chaofu Wu, Dr.<BR>> <BR>> xiaowu759@linux-s38y:~/workshop <BR>> <mailto:xiaowu759@linux-s38y:~/workshop>> pdb2gmx -f deta.pdb -o <BR>> deta.gro -p deta.top -i deta.itp -ter<BR>> :-) G R O M A C S (-:<BR>> Gromacs Runs One Microsecond At Cannonball Speeds<BR>> :-) VERSION 4.5.1 (-:<BR>> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,<BR>> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,<BR>> Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,<BR>> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,<BR>> Michael Shirts, Alfons Sijbers, Peter Tieleman,<BR>> Berk Hess, David van der Spoel, and Erik Lindahl.<BR>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<BR>> Copyright (c) 2001-2010, The GROMACS development team at<BR>> Uppsala University & The Royal Institute of Technology, Sweden.<BR>> check out http://www.gromacs.org for more information.<BR>> This program is free software; you can redistribute it and/or<BR>> modify it under the terms of the GNU General Public License<BR>> as published by the Free Software Foundation; either version 2<BR>> of the License, or (at your option) any later version.<BR>> :-) pdb2gmx (-:<BR>> Option Filename Type Description<BR>> ------------------------------------------------------------<BR>> -f deta.pdb Input Structure file: gro g96 pdb tpr etc.<BR>> -o deta.gro Output Structure file: gro g96 pdb etc.<BR>> -p deta.top Output Topology file<BR>> -i deta.itp Output Include file for topology<BR>> -n clean.ndx Output, Opt. Index file<BR>> -q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.<BR>> Option Type Value Description<BR>> ------------------------------------------------------<BR>> -[no]h bool no Print help info and quit<BR>> -[no]version bool no Print version info and quit<BR>> -nice int 0 Set the nicelevel<BR>> -chainsep enum id_or_ter Condition in PDB files when a new chain and<BR>> molecule_type should be started: id_or_ter,<BR>> id_and_ter, ter, id or interactive<BR>> -ff string select Force field, interactive by default. Use -h for<BR>> information.<BR>> -water enum select Water model to use: select, none, spc, spce,<BR>> tip3p, tip4p or tip5p<BR>> -[no]inter bool no Set the next 8 options to interactive<BR>> -[no]ss bool no Interactive SS bridge selection<BR>> -[no]ter bool yes Interactive termini selection, iso charged<BR>> -[no]lys bool no Interactive Lysine selection, iso charged<BR>> -[no]arg bool no Interactive Arganine selection, iso charged<BR>> -[no]asp bool no Interactive Aspartic Acid selection, iso charged<BR>> -[no]glu bool no Interactive Glutamic Acid selection, iso charged<BR>> -[no]gln bool no Interactive Glutamine selection, iso neutral<BR>> -[no]his bool no Interactive Histidine selection, iso checking<BR>> H-bonds<BR>> -angle real 135 Minimum hydrogen-donor-acceptor angle for a<BR>> H-bond (degrees)<BR>> -dist real 0.3 Maximum donor-acceptor distance for a H-bond <BR>> (nm)<BR>> -[no]una bool no Select aromatic rings with united CH atoms on<BR>> Phenylalanine, Tryptophane and Tyrosine<BR>> -[no]ignh bool no Ignore hydrogen atoms that are in the pdb file<BR>> -[no]missing bool no Continue when atoms are missing, dangerous<BR>> -[no]v bool no Be slightly more verbose in messages<BR>> -posrefc real 1000 Force constant for position restraints<BR>> -vsite enum none Convert atoms to virtual sites: none, hydrogens<BR>> or aromatics<BR>> -[no]heavyh bool no Make hydrogen atoms heavy<BR>> -[no]deuterate bool no Change the mass of hydrogens to 2 amu<BR>> -[no]chargegrp bool yes Use charge groups in the rtp file<BR>> -[no]cmap bool yes Use cmap torsions (if enabled in the rtp file)<BR>> -[no]renum bool no Renumber the residues consecutively in the <BR>> output<BR>> -[no]rtpres bool no Use rtp entry names as residue names<BR>> <BR>> Select the Force Field:<BR>> From current directory:<BR>> 1: CNT_OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<BR>> 2: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<BR>> From '/usr/local/gromacs/share/gromacs/top':<BR>> 3: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)<BR>> 4: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)<BR>> 5: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)<BR>> 6: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)<BR>> 7: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)<BR>> 8: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, <BR>> 1950-58, 2010)<BR>> 9: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)<BR>> 10: CHARMM27 all-atom force field (with CMAP) - version 2.0beta<BR>> 11: GROMOS96 43a1 force field<BR>> 12: GROMOS96 43a2 force field (improved alkane dihedrals)<BR>> 13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<BR>> 14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<BR>> 15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<BR>> 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<BR>> 17: [DEPRECATED] Encad all-atom force field, using full solvent charges<BR>> 18: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum <BR>> charges<BR>> 19: [DEPRECATED] Gromacs force field (see manual)<BR>> 20: [DEPRECATED] Gromacs force field with hydrogens for NMR<BR>> 16<BR>> Using the Oplsaa force field in directory oplsaa.ff<BR>> Opening force field file oplsaa.ff/watermodels.dat<BR>> Select the Water Model:<BR>> 1: TIP4P TIP 4-point, recommended<BR>> 2: TIP3P TIP 3-point<BR>> 3: TIP5P TIP 5-point<BR>> 4: SPC simple point charge<BR>> 5: SPC/E extended simple point charge<BR>> 6: None<BR>> 6<BR>> Opening force field file oplsaa.ff/aminoacids.r2b<BR>> Reading deta.pdb...<BR>> Read 20 atoms<BR>> Analyzing pdb file<BR>> Splitting PDB chains based on TER records or changing chain id.<BR>> There are 1 chains and 0 blocks of water and 1 residues with 20 atoms<BR>> chain #res #atoms<BR>> 1 ' ' 1 20 <BR>> All occupancies are one<BR>> Opening force field file oplsaa.ff/atomtypes.atp<BR>> Atomtype 1<BR>> <BR>> <BR><BR>-- <BR>========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR></DIV></:includetail>