Dear Gromacs user, Still another problem...
How can I manage the mutation upon a Trp? The mutation ALA-GLY does not cause any problem but the trasformation TRP-ALA seems uneasy. The Segmentation Fault error occurs suddenly I try to run the mdrun with lambda=1, with lambda=0.99 it take 6 step before to crash while if I start with lambda=0 it seems to work. So, I was thinking that it could be because the whole Trp rings, which loses lennard-jones interaction and charge, have still all its mass and this mass are connected on a single HB of the final alanine ( I'm using tha amber all-atom force field) that was the CG in the initial Trp. Could it be? Can how manage it somehow? Furthermore, if I change an aromatic residue in some long-sidechain amino acid how can I manage the dihedral and the bonds? I think I cannot let a bond disappear, for example if I try to transform a PHE in a LEU... Thank you for any hint you could give me! matteo > Date: Wed, 16 Jun 2010 15:17:30 +0200 > From: Matteo De Chiara <matn...@gmail.com> > Subject: Re: [gmx-users] FEP for amino acid mutations. > To: gmx-users@gromacs.org > Message-ID: > <aanlktikbum3htgngls6mo-cjl-buehpgeifdrhvk3...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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 >>> >>> >>> -- 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
