<table cellspacing='0' cellpadding='0' border='0' ><tr><td valign='top' style='font: inherit;'><P>Dear Dr. Lemkul,</P>
<P> </P>
<P>Thanks for the reply.</P>
<P>Yes I am referring to GROMOS forcefield. So how should i treat my partial charges. </P>
<P>Kindly advice.</P>
<P> </P>
<P>nahren<BR><BR>--- On <B>Fri, 7/11/08, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></P>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] Partial charges QM to GROMACS<BR>To: meetnahren@yahoo.com, "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Friday, July 11, 2008, 7:25 PM<BR><BR><PRE>Quoting nahren manuel <meetnahren@yahoo.com>:
> 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
jalemkul@vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================</PRE></BLOCKQUOTE></td></tr></table><br>