[AMBER] RMSD of different protein PDBs

From: Seibold, Steve Allan <stevesei.ku.edu>
Date: Sat, 27 Nov 2021 23:01:50 +0000

Hello Amber
I am trying to get a plot of a per residue RMSD of two separate proteins. I looked on-line in the AMBER files and looked at the manual. I have tried a few things; but, I am not confident that I am doing it correctly. I am using the following with cpptraj:

Parm protein1.prmtop
Trajin protein1.pdb
Reference protein2.pdb
Rmsd :1-690.CA,C,N,O perres perresout residue.dat perresmask :1-690.CA,C,N,O perresavg avgfile.dat

This does appear to work; but the data looks strange in the sense that from the N-terminus to the C-terminus there is substantial increase in the RMSD deviation. The two proteins I'm working with have a very similar fold and so, I am not convinced I am doing it properly.

Thanks, Steve

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Received on Sat Nov 27 2021 - 15:30:03 PST
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