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 [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
