[gmx-users] transfer of AMBER ion definitions to the ions.itp file

[OZGE ENGIN]

You are right, Justin. I simply incorporated the corresponding terms to the ions.itp file by relying on the definition types made for GROMOS and OPLS ffs.



-----Original Message-----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Sat, 29 Mar 2008 11:54:22 -0400
Subject: Re: [gmx-users] transfer of AMBER ion definitions to the ions.itp file

Quoting OZGE ENGIN <OZENGIN at KU.EDU.TR>:

> Hi all,
>
> I am trying to use AMBER96 ff under GROMACS package. I read the suggestions
> that were given at http://chemistry.csulb.edu/ffamber/.
> It has been stated that if any ion-related GROMACS tools will be used, then
> the AMBER ion definition to the ions.itp file should be added.
> So, does it mean that, I will copy the ions definitions that were given in
> the ffamber96.rtp file to the ions.itp file?
> I am a little bit confused because the definition of ions in AMBER is
> completely different from those of OPLS and GROMOS ff.

I don't see how these definitions are "completely different."  Use either of
these sections (OPLS or GROMOS) in ions.itp as a guide and add the appropriate
sections for AMBER96.  Using the OPLS definitions will be most directly
analogous in terms of how the atom types are defined.

-Justin

>
> Thanks in advance
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
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========================================

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/

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Ozge Engin
=================================
Computational Science & Engineering
Koc University