Great, got it, thanks for the suggestion, appreciate the input, Arneh
> 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. > > Yes. If you ask for an not-necessarily-physical result, you usually get > one... see http://wiki.gromacs.org/index.php/Average_Structure > >> 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.) > > "Correcting for" is not quite the right phrasing here... :-) It's > already correct according to the algorithm you used... it's not the > algorithm's fault you actually wanted a physical structure. One approach > you can use is to select the structure with the smallest RMSD from the > average, kind of like selecting the median as the central measure rather > than the mean of a numerical data set. Or you can take the nonphysical > structure and do EM on it... One needs to apply brain, of course! > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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 > _______________________________________________ gmx-users mailing list [email protected] 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
