On Wed, 14 Jan 2015 12:24:37 +0100
Federica Chiappori <federica.chiappori.itb.cnr.it> wrote:
> Dear Amber,
> I will perform a Free Energy Perturbation to evaluate the effect of a
> mutation. If I correctly understand the Amber module to perform FEP
> is the Gibbs module, but the last version including this module is
> the Amber7. It is possible to obtain this module separately?
> I have Amber 12 and Amber14 available, is there any other tool to
> perform FEP?
The newer versions now support TI only. Originally only in sander,
it is now also available in pmemd (since AMBER14). The A9 tutorial is a
bit dated now but still useful for basic information. Information for
the new pmemd code is in
http://pubs.acs.org/doi/abs/10.1021/ct400340s
(the supplement has input file example for a few standard cases).
Cheers,
Hannes.
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Received on Wed Jan 14 2015 - 04:00:03 PST
