Thank you very much for your reply Jason. Actually i want to calculate
single loop RMSD. This can be achieved only when i do fit other than loop
region and calculate the RMSD of that loop. Your advise works well for my
problem.
Thanks a lot.
Rajeswari. A
On Fri, Apr 1, 2011 at 1:14 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> The mask given in the RMSD command is what will be both fit AND calculated.
> I'm not exactly sure what you're trying to do, but what I think you're
> trying to do is fit based on one atom selection and calculate the RMSD
> based
> on a different atom selection. (Note that you can accomplish a fit on
> every
> atom NOT in a specific mask and then calculate the RMSD on everything IN
> that mask with this approach, if that's what you're trying to do).
>
> rms first mass <mask1>
> rms first mass out filename.dat <mask2> nofit
>
> This will fit to the first mask, then dump the RMSD values for each frame
> based on mask2 to filename.dat WITHOUT re-fitting to that mask.
>
> Hope this helps,
> Jason
>
> On Fri, Apr 1, 2011 at 12:03 AM, Rajeswari A.
> <rajeswari.biotech.gmail.com>wrote:
>
> > Dear Amber Users,
> >
> > I have a basic doubt in ptraj rmsd calculation.
> > 1. when we are giving mask residues for rmsd calculation, whether it
> > superimposes excluding the mask residues and find rmsd of that mask
> region?
> > 2. If not is there a way to do that in ptraj?
> >
> > I found MMTSB has this option. But i wanted to know in ptraj is there a
> > way?
> >
> > Thank you.
> >
> > Rajeswari. A
> > Research Scholar,
> > Computational Biophysics lab,
> > IIT Madras,
> > Chennai, India
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 01 2011 - 03:30:02 PDT
