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:
trajin....
reference....
rms reference subunit1 out backbone2.rmsd :1-60.CA,C,N
rms reference subunit2 out backbone2.rmsd :61-150.CA,C,N
etc.
...hope this helps...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 27 2018 - 15:30:02 PDT
