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

From: David A Case <>
Date: Tue, 27 Mar 2018 16:15:14 -0600

On Tue, Mar 27, 2018, Jag Silwal wrote:
> 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.

Try this:

   rms reference subunit1 out backbone2.rmsd :1-60.CA,C,N
   rms reference subunit2 out backbone2.rmsd :61-150.CA,C,N


...hope this helps...dac

AMBER mailing list
Received on Tue Mar 27 2018 - 15:30:02 PDT
Custom Search