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
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Received on Fri Apr 01 2011 - 01:00:02 PDT
