Dear Xiaojong,
We have not ported RAMD in newer versions of AMBER mainly due to the
lack of people/time ...
As it turned out that it is easier to implement RAMD in NAMD via NAMD's
flexible tcl scripting interface, I wrote the tcl scripts and now RAMD
is officially distributed with NAMD.
I would advise you to run your simulations with NAMD ... If you use the
AMBER force field, please read carefully this very nice page about using
the Amber ff in NAMD
http://ambermd.org/namd/namd_amber.html
Best wishes
Vlad
On 03/16/2012 10:02 AM, xiaojiong wrote:
> Dears,
> I want to identify egress routes for a ligand from a buried protein binding site,so I plan to use RAMD method.I know it only implemented in Amber8,but I can not find tutorial that use the RAMD?Can you give me some advice?Thanks!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Fri Mar 16 2012 - 04:00:03 PDT
