Re: [AMBER] pairwise RMSD

From: Mariano Rech <>
Date: Tue, 28 Jun 2011 11:35:12 +0200

Hi Mannan

do you mean that you have two trajectories? one of the bound and the other
of the unbound peptide?
If this is the case you can just join the two trajectories and calculate the
rmsd matrix of the joined trajectory you can do it easily with ptraj.
Eventually you can easily edit the output matrix to include just the parts
of pairwise rmsd of the different trajectories.

Hope this help

best regards

2011/6/28 Mannan <>

> Hi,
> Is there any way to calculate pairwise RMSD of bound and unbound peptides
> for a comparison.
> I would like to study the variations in conformations of the unbound with
> respect to the Bound,
> Thanks in Advance,
> Mannan
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Received on Tue Jun 28 2011 - 03:00:05 PDT
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