Hi, perhaps your .trr has some errors. Have you tried converting it or gmxcheck?
Other solution could be: Transfer your protein residues to an multiple pdb file and try do_dssp again. Perhaps your top or ndx doesn't fit. On Wednesday, 23. May 2007 17:07, Volker Knecht wrote: > Dear all, > > >Message: 4 > >Date: Wed, 23 May 2007 10:16:59 -0400 > >From: Justin Lemkul <[EMAIL PROTECTED]> > >Subject: Re: [gmx-users] Re: Re: do_dssp for many peptides > >To: Discussion list for GROMACS users <gmx-users@gromacs.org> > >Message-ID: <[EMAIL PROTECTED]> > >Content-Type: text/plain; charset=ISO-8859-1 > > > >>> do_dssp claims that are 248 residues in my selected group, although 248 > >>> is the number of *atoms* (not of residues) of this peptide. After the > >>> notion that some temporary file is backed up, do_dssp gets stuck again. > >>> > >>> I have even tried exactly Mark's suggestion (xtc file containing single > >>> peptide) for test reasons, but a similar problem occurs for the peptide > >>> denoted as chain N: do_dssp claims that are 124 residues in my selected > >>> group, although 124 is the number of *atoms* (not of residues) of this > >>> peptide. After the notion that some temporary file is backed up, > >>> do_dssp gets stuck again. > > > >I saw a similar description in the archives a long time ago when I was > > looking for help on do_dssp and experiencing similar problems (with a > > simpler system, granted). Which group are you selecting for running > > do_dssp? These errors seem to come up if you select any group other than > > 'MainChain' (choice 5, I believe). If do_dssp is finding an incorrect > > number of "residues," perhaps you have selected 'Protein' instead of > > 'MainChain' for your analysis? > > Thanks for your reply, Justin. Indeed I had chosen 'Protein' so far. But > it is not evident that this caused the problem, since it worked well in > some cases. Indeed, choosing 'MainChain' (indeed index group 5) does not > help, but results in the same behavior. > > Volker Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
