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" <[email protected]> > Subject: RE: [gmx-users] FEP for amino acid mutations. > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <[email protected]> > 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 > [email protected] > +61 3 9903 9167 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble > a nail. > >> -----Original Message----- >> From: [email protected] [mailto:gmx-users- >> [email protected]] On Behalf Of Matteo De Chiara >> Sent: Monday, 14 June 2010 8:05 PM >> To: [email protected] >> 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
