Dear all,
Yet another question on the use of different modified versions of the
ff99sb force field in AMBER12 ...
We are currently using ff99SB+pbsc0+ildn+Brueschweiler(NMR-based)
modifications.
This relies on very old parameter dataset parm99.dat on top of which the
frcmods of the modifications are added.
While trying to change the set of ion parameters, we noticed that
loading an old parameter data set can lead to errors in which the added
parameters in the frcmod files were not correctly implemented in the
topology files.
Now, when trying to move to using ff10 by loading parm10.dat and all the
corresponding libraries, I realized that the ff10 is not compatible with
the ILDN and Brueschweiler modifications. One of the reason for this
incompatibility is because the Calpha atoms have now a CX atom type ...
My goal is to use the following force field: ff10 + ILDN +
Best&Hummer(NMR-nased modifications).
The latter modifications are not even included with AMBER, which is
rather unfortunate because D.E. Shaw and co-workers has shown that this
combination leads to the best results in folding simulations among the
AMBER variants (2012 PLoS One publication)...
Does anybody use this combination in AMBER and is willing to share the
corresponding files ? Did anybody compare Brueschweiler modification
with the ones from Best&Hummer ?
Thank you very much for any thoughts on this ...
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 Thu Mar 28 2013 - 04:00:03 PDT
