[AMBER] ion parameters in simulations with nucleic acids

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Thu, 05 Apr 2012 13:54:12 +0200

Dear Ambers,

I would like to ask for an advice regarding which ion parameters to be
used in simulations of nucleic acids.

Since the new parameters from Tom Cheatham's work were added to AMBER we
used those parameters in the simulations. However, recently I came
across a paper coming from Modesto Orozco's group (PCCP 2009), showing
that these parameters are less suitable than for examples Dang's
parameters in simulations with nucleic acids.

I'd appreciate some (recent) thoughts on this issue.

Also, I would like to ask if somebody has the leap libraries and
parameters for Dang's parameters. I could not find them neither in the
AMBER distribution nor in the contributed parameters. I hope I am not
too blind here ...

Best wishes

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 Thu Apr 05 2012 - 05:00:04 PDT
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