[gmx-users] Partial charges QM to GROMACS

[Justin A. Lemkul]

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 <meetnahren at yahoo.com>:

> 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 <jalemkul at vt.edu> wrote:
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Partial charges QM to GROMACS
> To: meetnahren at yahoo.com, "Discussion list for GROMACS users"
> <gmx-users at gromacs.org>
> Date: Friday, July 11, 2008, 7:25 PM
>
> Quoting nahren manuel <meetnahren at 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 at vt.edu | (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
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================