Hi. <div><br></div><div>I seem having some problem in running ./pdb2gmx. Here is the output file. Can you help me in giving me some idea to deal with this?</div><div><br></div><div><span class="Apple-style-span" style="border-collapse: collapse; white-space: nowrap; -webkit-border-horizontal-spacing: 2px; -webkit-border-vertical-spacing: 2px; "><div>
bcsb09s-imac52:bin bcsb09$ pdb2gmx -f 1aml.pdb -p 1aml.top -o 1aml.gro</div><div> :-) G R O M A C S (-:</div><div><br></div><div> Getting the Right Output Means no Artefacts in Calculating Stuff</div>
<div><br></div><div> :-) VERSION 3.3.3 (-:</div><div><br></div><div><br></div><div> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.</div><div> Copyright (c) 1991-2000, University of Groningen, The Netherlands.</div>
<div> Copyright (c) 2001-2008, The GROMACS development team,</div><div> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.</div><div><br></div><div> This program is free software; you can redistribute it and/or</div>
<div> modify it under the terms of the GNU General Public License</div><div> as published by the Free Software Foundation; either version 2</div><div> of the License, or (at your option) any later version.</div>
<div><br></div><div> :-) pdb2gmx (-:</div><div><br></div><div>Option Filename Type Description</div><div>------------------------------------------------------------</div><div>
-f 1aml.pdb Input Generic structure: gro g96 pdb tpr tpb tpa</div><div> xml</div><div> -o 1aml.gro Output Generic structure: gro g96 pdb xml</div><div> -p 1aml.top Output Topology file</div>
<div> -i posre.itp Output Include file for topology</div><div> -n clean.ndx Output, Opt. Index file</div><div> -q clean.pdb Output, Opt. Generic structure: gro g96 pdb xml</div><div><br></div><div>
Option Type Value Description</div><div>------------------------------------------------------</div><div>-[no]h bool no Print help info and quit</div><div>-nice int 0 Set the nicelevel</div>
<div>-[no]merge bool no Merge chains into one molecule definition</div><div>-ff string select Force field, interactive by default. Use -h for</div><div> information.</div><div>
-water enum spc Water model to use: with GROMOS we recommend SPC,</div><div> with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p</div><div> or f3c</div><div>-[no]inter bool no Set the next 6 options to interactive</div>
<div>-[no]ss bool no Interactive SS bridge selection</div><div>-[no]ter bool no Interactive termini selection, iso charged</div><div>-[no]lys bool no Interactive Lysine selection, iso charged</div>
<div>-[no]arg bool no Interactive Arganine selection, iso charged</div><div>-[no]asp bool no Interactive Aspartic Acid selection, iso charged</div><div>-[no]glu bool no Interactive Glutamic Acid selection, iso charged</div>
<div>-[no]gln bool no Interactive Glutamine selection, iso neutral</div><div>-[no]his bool no Interactive Histidine selection, iso checking</div><div> H-bonds</div><div>-angle real 135 Minimum hydrogen-donor-acceptor angle for a</div>
<div> H-bond (degrees)</div><div>-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)</div><div>-[no]una bool no Select aromatic rings with united CH atoms on</div>
<div> Phenylalanine, Tryptophane and Tyrosine</div><div>-[no]ignh bool no Ignore hydrogen atoms that are in the pdb file</div><div>-[no]missing bool no Continue when atoms are missing, dangerous</div>
<div>-[no]v bool no Be slightly more verbose in messages</div><div>-posrefc real 1000 Force constant for position restraints</div><div>-vsite enum none Convert atoms to virtual sites: none, hydrogens</div>
<div> or aromatics</div><div>-[no]heavyh bool no Make hydrogen atoms heavy</div><div>-[no]deuterate bool no Change the mass of hydrogens to 2 amu</div><div><br></div><div>Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat</div>
<div><br></div><div>Select the Force Field:</div><div> 0: GROMOS96 43a1 force field </div><div> 1: GROMOS96 43b1 vacuum force field</div><div> 2: GROMOS96 43a2 force field (improved alkane dihedrals)</div><div> 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)</div>
<div> 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) </div><div> 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) </div><div> 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)</div><div> 7: Encad all-atom force field, using scaled-down vacuum charges</div>
<div> 8: Encad all-atom force field, using full solvent charges </div><div>2</div><div>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp</div><div>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat</div>
<div>Reading 1aml.pdb...</div><div>Read 'AMYLOID A4', 598 atoms</div><div>Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat</div><div>26 out of 26 lines of xlateat.dat converted succesfully</div>
<div>Analyzing pdb file</div><div>There are 1 chains and 0 blocks of water and 40 residues with 598 atoms</div><div><br></div><div> chain #res #atoms</div><div> 1 ' ' 40 598 </div><div><br></div><div>All occupancies are one</div>
<div>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.atp</div><div>Atomtype 50</div><div>Reading residue database... (ffG43a2)</div><div>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.rtp</div>
<div>Residue 96</div><div>Sorting it all out...</div><div>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2.hdb</div><div>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-n.tdb</div><div>Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a2-c.tdb</div>
<div><br></div><div>-------------------------------------------------------</div><div>Program pdb2gmx, VERSION 3.3.3</div><div>Source code file: futil.c, line: 313</div><div><br></div><div>File input/output error:</div><div>
1aml.top</div><div>-------------------------------------------------------</div><div><br></div><div>I seem to be having problem in running the test tun as well. Below is its output: </div><div><br></div><div><div>bcsb09s-imac52:bin bcsb09$ ./gmxtest.pl</div>
<div>Usage: ./gmxtest.pl [ -np N ] [-verbose ] [ -double ] [ simple | complex | kernel | pdb2gmx | all ]</div><div> or: ./gmxtest.pl clean | refclean | dist</div><div><br></div></div><div>Thanks..</div><div><br></div><div>
Best regards,</div><div>Joyce</div></span></div>