AMBER Archive (2005)

Subject: Re: AMBER: RMSD Calculations

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Mon Dec 05 2005 - 10:00:23 CST

for ptraj you do indeed need to have the same number of atoms
in the reference structure as you have in the prmtop that you load into
ptraj.
if you can get that resolved then the other issues would be ok.

Kara Di Giorgio wrote:

>
>
> I'm also worried that it will only calculate the RMSD if there are an
> identical number of atoms in each, which I don't have.
>

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