Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. If you use QM as a start, be prepared to refine your charges a lot until you replicate experimentally-observed behavior. Nonpolar groups are usually given zero charge anyway, because of the use of charge groups (another problem with starting from QM). Another idea for Gromos parameters would be to use PRODRG beta to give you an initial topology, but be prepared to make some refinements to the charges and charge groups there too!
I think you would benefit from reading the original papers about Gromos force field derivation. Some links are available on the Gromacs wiki site. -Justin Quoting nahren manuel <[EMAIL PROTECTED]>: > Dear Dr. Lemkul, > > Thanks for the reply. > Yes I am referring to GROMOS forcefield. So how should i treat my partial > charges. > Kindly advice. > > nahren > > --- On Fri, 7/11/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Partial charges QM to GROMACS > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > <[email protected]> > Date: Friday, July 11, 2008, 7:25 PM > > 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/ > > ======================================== > > > ======================================== 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
