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.
Mark
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 [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
