<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>2 apr 2012 kl. 16.02 skrev lina:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila <<a href="mailto:oinanki@gmail.com">oinanki@gmail.com</a>> wrote:<br><blockquote type="cite">We are trying to do simulation of lysozyme in water.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">step with problem : energy minimization.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c<br></blockquote><blockquote type="cite">1AKI_solv_ions.gro -p topol.top -o em.tpr<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> :-) G R O M A C S (-:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Getting the Right Output Means no Artefacts in Calculating Stuff<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> :-) VERSION 4.0.5 (-:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br></blockquote><blockquote type="cite"> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br></blockquote><blockquote type="cite"> Copyright (c) 2001-2008, The GROMACS development team,<br></blockquote><blockquote type="cite"> check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> This program is free software; you can redistribute it and/or<br></blockquote><blockquote type="cite"> modify it under the terms of the GNU General Public License<br></blockquote><blockquote type="cite"> as published by the Free Software Foundation; either version 2<br></blockquote><blockquote type="cite"> of the License, or (at your option) any later version.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> :-) grompp (-:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Option Filename Type Description<br></blockquote><blockquote type="cite">------------------------------------------------------------<br></blockquote><blockquote type="cite"> -f minim.mdp Input, Opt! grompp input file with MD parameters<br></blockquote><blockquote type="cite"> -po mdout.mdp Output grompp input file with MD parameters<br></blockquote><blockquote type="cite"> -c 1AKI_solv_ions.gro Input Structure file: gro g96 pdb tpr tpb<br></blockquote><blockquote type="cite">tpa<br></blockquote><blockquote type="cite"> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br></blockquote><blockquote type="cite"> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br></blockquote><blockquote type="cite"> -n index.ndx Input, Opt. Index file<br></blockquote><blockquote type="cite"> -p topol.top Input Topology file<br></blockquote><blockquote type="cite"> -pp processed.top Output, Opt. Topology file<br></blockquote><blockquote type="cite"> -o em.tpr Output Run input file: tpr tpb tpa<br></blockquote><blockquote type="cite"> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt<br></blockquote><blockquote type="cite"> -e ener.edr Input, Opt. Energy file: edr ene<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Option Type Value Description<br></blockquote><blockquote type="cite">------------------------------------------------------<br></blockquote><blockquote type="cite">-[no]h bool no Print help info and quit<br></blockquote><blockquote type="cite">-nice int 0 Set the nicelevel<br></blockquote><blockquote type="cite">-[no]v bool yes Be loud and noisy<br></blockquote><blockquote type="cite">-time real -1 Take frame at or first after this time.<br></blockquote><blockquote type="cite">-[no]rmvsbds bool yes Remove constant bonded interactions with virtual<br></blockquote><blockquote type="cite"> sites<br></blockquote><blockquote type="cite">-maxwarn int 0 Number of allowed warnings during input<br></blockquote><blockquote type="cite">processing<br></blockquote><blockquote type="cite">-[no]zero bool no Set parameters for bonded interactions without<br></blockquote><blockquote type="cite"> defaults to zero instead of generating an error<br></blockquote><blockquote type="cite">-[no]renum bool yes Renumber atomtypes and minimize number of<br></blockquote><blockquote type="cite"> atomtypes<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#<br></blockquote><blockquote type="cite">checking input for internal consistency...<br></blockquote><blockquote type="cite">processing topology...<br></blockquote><blockquote type="cite">Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp<br></blockquote><blockquote type="cite">Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp<br></blockquote><blockquote type="cite">Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp<br></blockquote><blockquote type="cite">Generated 332520 of the 332520 non-bonded parameter combinations<br></blockquote><blockquote type="cite">Generating 1-4 interactions: fudge = 0.5<br></blockquote><blockquote type="cite">Generated 332520 of the 332520 1-4 parameter combinations<br></blockquote><blockquote type="cite">Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp<br></blockquote><blockquote type="cite">Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp<br></blockquote><blockquote type="cite">Excluding 3 bonded neighbours molecule type 'Protein_A'<br></blockquote><blockquote type="cite">Excluding 2 bonded neighbours molecule type 'SOL'<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-------------------------------------------------------<br></blockquote><blockquote type="cite">Program grompp, VERSION 4.0.5<br></blockquote><br>You use Version 4.0.5.<br><br>If I remember correctly, the earlier version has different pname.<br>(seems one is NA+, one is NA)<br><br>If I were you, I would update to latest version and try.<br></div></blockquote><div><br></div><div>Upgrading may be a good thing for many reasons. To see what are the names of ions, check ions.itp.</div><br><blockquote type="cite"><div><br><blockquote type="cite">Source code file: toppush.c, line: 1641<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Fatal error:<br></blockquote><blockquote type="cite">No such moleculetype NA<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">what should we do????<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite">Please search the archive at<br></blockquote><blockquote type="cite"><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
</div>
<br></body></html>