Re: [AMBER] RMSD for two trajectories

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 22 Dec 2010 15:45:05 -0800

> I have two trajectories of MD simulation related to wild type
> and mutant form of my ligand in the complex of<A0>receptor-ligand.
> I would like to compare the RMSD of pairwise structures but<A0>I
> have not found any option in VMD in order to do that. How can I
> compare the RMSD of two seperate trajectories.

I believe this is not an existing ptraj capability. If so, unless
there is a non-Amber program that you could e.g. feed pairs of pdb
files to, I think you will need to do some programming to make that
happen. The tricky part would be if the two forms are not chemically
identical. In this case, you'd need to read in two prmtops and
just align/measure the parts that are the same.


AMBER mailing list
Received on Wed Dec 22 2010 - 16:00:03 PST
Custom Search