Re: [AMBER] RMSD between two different proteins

From: Jagan Mohan <>
Date: Fri, 19 Mar 2010 12:56:37 +0530

Hey nicholus,

You can do that using the RMSD Trajectory Tool in VMD 1.8.7. I hope that
answered ur question. You can also do the same thing in ptraj.


On Fri, Mar 19, 2010 at 12:40 PM, nicholus bhattacharjee <> wrote:

> Dear community,
> We know that rms command in ptraj can be used to
> calculated the RMSD of different snapshot with respect to some given
> structure. Agani some visual sofwares like pymol can be used to calculate
> RMSD between two different protein structures a.pdb and b.pdb. Now my query
> is that is there a way to find the RMSD of different snapshot of b.pdb
> simulation structure from a.pdb i.e at various time step I want to
> calculate
> the deviation of structure of b.pdb from a.pdb. Thanx in advance for
> answering.
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list

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Received on Fri Mar 19 2010 - 00:30:04 PDT
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