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.
matteo > > Message: 5 > Date: Tue, 15 Jun 2010 08:53:25 +1000 > From: "Dallas B. Warren" <dallas.war...@pharm.monash.edu.au> > Subject: RE: [gmx-users] FEP for amino acid mutations. > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <89907ea1dcfb7548a431c13a270f9dd50ad84...@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.war...@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-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] On Behalf Of Matteo De Chiara >> Sent: Monday, 14 June 2010 8:05 PM >> To: gmx-users@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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
