Quoting Jens Pohl <[EMAIL PROTECTED]>: > > > -----Ursprüngliche Nachricht----- > > Von: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Gesendet: 12.01.08 03:29:49 > > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Betreff: Re: [gmx-users] Problems with GROMPP > > > > > > > > > It seems, that my protein is truncated in the xxx.gro file. The number of > water molecules is ok, but there are about 150 AS residues missing after I > run GENBOX ??? The xxx.top has them included, so this explains the different > numbers. > > > > Well, read the warning messages from pdb2gmx, genbox and grompp carefully. > > > > Mark > > I didn't receive any warnings going through the single steps. No problem with > pdb2gmx. When I compare the *.gro to the original file there seems to be > everything ok. Same with editconf. (I rerun pdb3gmx and used -q to get a > *.pdb to compare to my original one). When I run genbox I get the *.top with > all residues, but the *.gro is truncated. Did it several times with the same > result...but no massage, that anything might be wrong (or I was too tired to > see it. Will do it again tomorrow)
It might be helpful to post to the list the exact commands you issued so far. It might be illustrative of the problem. -Justin > > Jens > > > __________________________________________________________________________ > Erweitern Sie FreeMail zu einem noch leistungsstärkeren E-Mail-Postfach! > Mehr Infos unter http://produkte.web.de/club/?mc=021131 > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php