[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.
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
> -----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!
> Ph.D. Student
> Matteo De Chiara
> Dept. of Molecular Biology, University of Siena
> Via Fiorentina 1,
> 53100 Siena Italy
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