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i want to ask you question about how can i deprotonate or use deprotonated cysteine because I have protein with “cys” in active site, and I want to use deprotonated<BR>“cys”. when i run “pdb2gmx “ no option appearing of choosing Cys deprotonated state possibility <BR><BR>> Date: Sun, 27 Jul 2008 13:16:20 +0200<BR>> From: spoel@xray.bmc.uu.se<BR>> To: gmx-users@gromacs.org<BR>> Subject: Re: [gmx-users] number of grid cells is zero<BR>> <BR>> N. Sundar Ram wrote:<BR>> > Hi everyone,<BR>> > I am a new user of gromacs. I am running MD for a Pleckstrin<BR>> > homology domain (100 amino acids) in 8 nodes (32 CPUs). After<BR>> > Mdurn i get the following error: "Number of grid cells is<BR>> > zero. system is collapsing".<BR>> > Though I saw many mails regarding this problem in the mailing list, I<BR>> > could not get a proper answer.<BR>> > <BR>> > Can anyone please tell me what should I do to get it running.<BR>> > <BR>> > Thanking you in advance.<BR>> fix the problems in your structure most likely. Did you say homology?<BR>> check the wiki.<BR>> <BR>> -- <BR>> David van der Spoel, Ph.D., Professor of Biology<BR>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<BR>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<BR>> spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<BR><br /><hr />Téléchargez le nouveau Windows Live Messenger ! <a href='http://get.live.com/messenger/overview' target='_new'>Téléchargez Messenger, c'est gratuit !</a></body>
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