<DIV>Dear gmx-users,</DIV>
<DIV> 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.</DIV>
<DIV> Chaofu Wu, Dr.</DIV>
<DIV> </DIV>
<DIV><A href="mailto:xiaowu759@linux-s38y:~/workshop">xiaowu759@linux-s38y:~/workshop</A>> pdb2gmx -f deta.pdb -o deta.gro -p deta.top -i deta.itp -ter<BR> :-) G R O M A C S (-:</DIV>
<DIV> Gromacs Runs One Microsecond At Cannonball Speeds</DIV>
<DIV> :-) VERSION 4.5.1 (-:</DIV>
<DIV> 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,</DIV>
<DIV> Berk Hess, David van der Spoel, and Erik Lindahl.</DIV>
<DIV> 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 <A href="http://www.gromacs.org">http://www.gromacs.org</A> for more information.</DIV>
<DIV> 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.</DIV>
<DIV> :-) pdb2gmx (-:</DIV>
<DIV>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.</DIV>
<DIV>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 (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 output<BR>-[no]rtpres bool no Use rtp entry names as residue names</DIV>
<DIV><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, 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 charges<BR>19: [DEPRECATED] Gromacs force field (see manual)<BR>20: [DEPRECATED] Gromacs force field with hydrogens for NMR<BR>16</DIV>
<DIV>Using the Oplsaa force field in directory oplsaa.ff</DIV>
<DIV>Opening force field file oplsaa.ff/watermodels.dat</DIV>
<DIV>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</DIV>
<DIV> chain #res #atoms<BR> 1 ' ' 1 20 </DIV>
<DIV>All occupancies are one<BR>Opening force field file oplsaa.ff/atomtypes.atp<BR>Atomtype 1</DIV>
<DIV> </DIV>