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

[Justin A. Lemkul]

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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



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

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/

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