[gmx-users] FEP for amino acid mutations.

Matteo De Chiara matnamo at gmail.com
Wed Jun 16 15:17:30 CEST 2010

Thank you!
I tried to change from Ala to Gly in aqueous environment and seems to
have worked well. Now I will try to change a Trp, the amino acid  I
have to apply the real mutation.


> Message: 5
> Date: Tue, 15 Jun 2010 08:53:25 +1000
> From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au>
> Subject: RE: [gmx-users] FEP for amino acid mutations.
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <89907EA1DCFB7548A431C13A270F9DD50AD84269 at prk-exch-01.vcp.local>
> Content-Type: text/plain; charset=us-ascii
> 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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