[AMBER] RMSD of individual sub unit of a protein complex.

From: Jag Silwal <jagsilwal.gmail.com>
Date: Tue, 27 Mar 2018 17:40:20 -0400

Dear all,

I have a protein complex with 4 subunits and I calculated the RMSD using

trajin final.mdcrd
reference minimized.pdb
rms reference out backbone2.rmsd .CA,C,N

There is a big jump in RMSD at some point and I would like to calculate
RMSD for each subunit separately to see if the RMSD jump is mainly because
of Protein-protein interacting.

It should be simple and I tried to follow the tutorial but I don't think I
am getting this right. The first subunit is 60 residues long from 1- 60,
second is from 61-150 ...so on. How do I individually calculate RMSD from
the simulation of this complex?

I would really appreciate your quick response on this as I am kind of stuck
at the last moment before a presentation.

Thank you in advance.

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Received on Tue Mar 27 2018 - 15:00:03 PDT
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