Quoting nahren manuel <[EMAIL PROTECTED]>: > Dear Gromacs Users, > > 1. I calculated the partial charges of my ligand using QM. Since GROMACS > ignores the non-polar hydrogen, is it a good approximation to include the > charges as it is from QM method to my ligand heavy atoms ?.
Gromacs does no such thing! What you're referring to is the *Gromos* force field, which is an entirely separate idea. There are all-atom force fields for use with Gromacs - OPLS, Amber, and even CHARMM, if you're adventurous :-) What you need to be concerned with is whether or not these QM charges and methodology are compatible with your force field of choice. > > 2. should i adjust that partial charges , If so how to do the same? See above. -Justin > > regards, > nahren > > > > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
