Hi, On Thursday, 20. September 2007 16:15, Arneh Babakhani wrote: > Hi, > > When outputting the average structure from g_rmsf using the -ox option, > some of my residues in that average structure pdb have awkward coordinates > (when you visualize it in VMD, it looks very strange). Sometimes atoms > are placed very close to each other, with really bad bond angles. I > suppose this is a facet of the averaging scheme in g_rmsf. > > Is there a way to correct for this, and to obtain an averagestructure.pdb > that looks more reasonable coordinates and bond angles? (I ask b/c I'd > like to use this averagestructure.pdb in further studies, such as > docking.)
this is the normal problem, when looking at average structures. Easiest is to minimize the structure again, depends on your strucure you have perphaps to restrain backbone atoms. > > thanks, > > Arneh > > > _______________________________________________ > 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 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
