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/ ========================================
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