Hi Jo, You're using 3.2.1? The first query is for the group to use for fitting, then you're asked for how many groups you want the RMSD and subsequently asked to give the groups. So the RMSD you get for resid162 is probably what you want.
With version 3.3.1 you can also fit the trajectory using trjconv and use g_rms with the option -fit none, in which case it will only ask for one group to determine the RMSD for. Hope it helps, Tsjerk On 8/27/07, jo hanna <[EMAIL PROTECTED]> wrote: > Hi > > What I want to do is to calculate the RMSD of one binding pocket residue of > my protein after fitting to the Ligand in my simulation. > > I have tried the following using g_rms: > > selecting 12 LIG > groups to compare 2 > selecting 12 LIG > selecting 16 resid162 > > But I don't know if this is the doing the correct thing, or if this is the > correct way to do this. > Could anyone please advise? > > Thanks > Jo > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] http://www.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
