Hi, The setting of partial charges is a delicate matter. How you do it depends on your ligand, the force-field you use and computational power available to you. If you're just simulating a single protein, than I would use an ab-initio of DFT potential rather than semi-empirical one such (which is what MOPAC gives you). In general, I would try to work as the force-field developers did in developing the charges - which means that RESP would be the method of choice for AMBER but not necessarily for different FFs.
You have free software that you can use for such calculations such as GAMESS-US and NW-CHEM (though you need to obtain a licence to use them). Ran. raja wrote: > Hi gmxions, > > I have found many article for calculating partial charges for a ligand > using RESP (restricted electro static fitting) within active site using > gaussian. But I do not have gaussion, So Is it done also by MOPAC? And > if it is so kindly refer me the protocol to do that. > > With thanks! > B.Nataraj > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ 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
