Dear Gromacs users, I intend to perform a MD simulation of a GPCR model applying distant restraints to the backbone of alpha helices, something like NOE distance restraints. I guess that gromacs can't do it directly but if I've well understand I can manually provide classical distance restraints instead of NOE. My matter is that my model is based on a X-Ray structure and I've not experience in NMR, so I feel unsure about the idea. I've three questions: Does anybody know if there is a dataset of standard or statistical distance restraints for typical secondary structures to use as a template (I need to fix Hbonds between helical turns)? Or should I better define arbitrary distances assuming a Hbond cutoff? Given that the NMR structure of my template has been published but is firmly worse than the X-Ray one, should I looking for experimental data about it?
Thanks in advance Chiara _______________________________________________ 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
