Hi,
sounds like you could start with MMPBSA which is useful for binding
energies or use thermodynamic integration which is FEP-like. Both methods
are detailed in the manual and tutorials.
Thomas
On Fri, April 29, 2011 12:41 am, Chirag Vora wrote:
> Dear AMBER users and developers,
> I am calculating free energy of interaction between a small molecule and a
> polymer. To achieve this I want to adopt *Free Energy Perturbation
> (FEP) *approach.
> This method was frequently reported in literature in 90's and suffered a
> drawback of slow convergence.
> Up to AMBER 7 "Gibbs" module was used to perform FEP.
>
> My question is whether or not it is possible to perform Free Energy
> Perturbation using AMBER 10.
> If yes, which module can be used in AMBER 10 to do the same?
> Thanks in advance.
> --
> Chirag V. Vora <chiragvora.live.com>
> Department of Pharmacoinformatics
> <http://pharmacoinformatics.tripod.com/>,
> Natnl. Inst. of Pharm. Edu. and Res. (NIPER) <http://niper.ac.in>
> *Sector 67, S.A.S. Nagar, *
> *Punjab (INDIA) - 160 062, *
> *Phone: +91-9814187740*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Apr 29 2011 - 02:00:04 PDT
