Hi all, Energy minimization of two proteins, two are same protein but differing in form in which it is available in PDB (ligand bound and bare active site). There are no different in secondary structure extension between these two proteins according to experimental structure. When I minimize these two proteins using Gromacs minimization engine, a part of the secondary structure in protein with bound ligand is lost (here secondary structure is referring a Helix), coincidently that is the region of interest for my study. That is, the mutant variant at that position having a role in substrate conversion effect. I repeated the protocol of minimization with more rigorous using more stringent parameter set but there is no effect. This is really adding more interest to my work. I feel that I got result even before the most rigorous part of real MD itself. Is it really some thing to be existed about? And is it something that Gromacs engine had found out, the imperfection in crystallographic solved structure. Kindly share similar experience, one had in this list, would be so interesting to hear and feel good about my on going work.
With regards, B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - I mean, what is it about a decent email service? _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
