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

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 29 16:54:22 CET 2008


> 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.


> 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


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