[gmx-users] FEP for amino acid mutations.

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Tue Jun 15 00:53:25 CEST 2010

I would make a new residue in the .rtp file.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Matteo De Chiara
> Sent: Monday, 14 June 2010 8:05 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] FEP for amino acid mutations.
> Dear GROMACS users,
> I would like to perform a FEP calculation mutating a residue outside
> the active site of a protein.
> I was wondering if I have to create a .itp file for the mutation or it
> is possible to modify the .rtp file ( adding the state B parameter to
> the amino acid I would like to change). Of course, in this case, I
> will create a new amino acid type identical to the one I would like to
> mutate in order to act only on the amino acid in a specific position.
> Thanks for your help!
> matteo
> --
> Ph.D. Student
> Matteo De Chiara
> Dept. of Molecular Biology, University of Siena
> Via Fiorentina 1,
> 53100 Siena Italy
> --
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