Dear Amber users,
I am looking into starting simulations of a protein that has a GDP and a
MG ion in the active site.
I know that in the database of AMBER parameters there are the Carlson
parameters for GDP and the new Sorensen parameters for MG.
I also found this comment from David Case which made me wonder about
GDP. Is there anything new on the paper mentioned there ?
http://archive.ambermd.org/201112/0208.html
I also read carefully this thread.
http://archive.ambermd.org/201205/0530.html
Before starting simulations, I would be very grateful if people that
have been using these parameter sets would comment on their experience
with them (besides what is published in the respective references).
If people are aware of other parameter sets, not available in the data
base but worth trying out, I would also be very interested.
Best wishes
Vlad
--
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
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Mon Aug 27 2012 - 01:30:03 PDT
