Hi Ran, Thanks for your suggestion. B.Nataraj On Fri, 10 Nov 2006 09:16:29 +0100, "Ran Friedman" <[EMAIL PROTECTED]> said: > 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 gmx-users@gromacs.org > 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 -- raja [EMAIL PROTECTED]
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