Perhaps this can help you Christopher M. Summa and Michael Levitt Near-native structure refinement using in vacuo energy minimization PNAS 2007 104: 3177-3182; published online before print as 10.1073/pnas.0611593104
Marcos On Wed, 2007-04-25 at 14:46 +0400, dimitry.a.suplatov wrote: > Hello. > I'm doing homology modeling. My model after MODELLER has Ramachandran > Z-score = 0.7 (that is OK). Then Im doing energy minimization with > steep, emtol=200 KJ/mol*nm. Fmax was converged to 1.82684e+02 in about > 4000 steps. Backbone RMS compared to MODELLER model is 0.27nm. Z-score > is -3.5 and that is very poor. > Questions: > 1. Could 4000 steps be too much for minimization? May be I should use > not more than 1000 and do not care about Fmax? > 2. What minimization protocol do you prefer? What about using different > alorythms step by step? > > Thank you. > Dimitry. > > _______________________________________________ > 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 _______________________________________________ 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
