[gmx-users] spc.itp for the amber force field

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 4 02:47:47 CEST 2009

Rebeca García Fandiño wrote:
> Hi,
> I am trying to simulate a system using the parameters for ions developed 
> by Joung et al. and implemented in Amber (frcmod.ionsjc_spce).
> I have the topology and the crd file. Now, I want to obtain the topology 
> for Gromacs using amb2gmx.pl, so I must change the default parameters 
> (for tip3p) included in amb2gmx.pl.
> I have seen that in the .tar file ffamber_v4.0 there is no a 
> corresponding itp file for spc model of water in amber, so what 
> parameters should I include for the section of bondtypes, angletypes, 
> atoms, bonds, angles, settles,...? Those corresponding to the SCP in 
> Gromacs directly?

Maybe. The required form for the nonbonded parameters depends on 
combination rules in force. First you should find out if SPC should work 
with AMBER, because literature that says that will probably also specify 
the parameters.

Perhaps simpler is use amb2gmx.pl to convert the non-solvent part, and 
then solvate with genbox and add ions with genion later. You'd still 
need SPC parameters for AMBER however.


> Thank you very much for your help.
> Best wishes,
> Rebeca Garcia
> Academic Visitor
> Oxford University
> ------------------------------------------------------------------------
> Charlas más divertidas con el nuevo Windows Live Messenger 
> <http://download.live.com>
> ------------------------------------------------------------------------
> _______________________________________________
> 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

More information about the gromacs.org_gmx-users mailing list