Ok, thanks, I figured as much, was wondering if there was an option perhaps in g_rmsf that would produce a "minimized" average structure . . . I guess not,
Arneh > 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) â 9131 â 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
