Perfect! Hadn't thought of that! Was hoping to look at side chain fluctuations as well, but I think if I have the c-alpha comparison to WT and then side chain comparison to self, that should work well.
Thanks for your help!!! Natalie ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Erik Marklund [erik.markl...@chem.ox.ac.uk] Sent: 07 September 2015 11:42 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] RMSD comparison to a different reference structure. Hi, How about comparing only C-alphas? As long as you have the same number of residues, that should work. You need to make reduced versions of your tpr and trajectory files. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ > On 7 Sep 2015, at 09:32, Natalie Stephenson > <natalie.stephen...@manchester.ac.uk> wrote: > > > > Hi, > > I was wondering if you would be able to advise me of the best method to > compare a mutated and WT structure. I was hoping to perform RMSD analysis for > certain regions within a mutation against the same region within the wild > type structure. Unfortunately, the atom numbering is likely to be off for > some regions, as the mutation with add/remove atoms. As only one index file > is specified for the g_rms command I wondered how best to do this? Or if it > was possible? > > Thanks, > Natalie > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
