[gmx-users] g_rms: fitting to one residue whilst measuring rmsd of another

[Tsjerk Wassenaar]

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 <jfhanna at gmail.com> 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
>
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-- 
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