[AMBER] RMSD of single residue, fit to main structure

From: Rosellen, Martin <martin.rosellen.16.ucl.ac.uk>
Date: Mon, 4 Feb 2019 14:33:18 +0000

Dear all,

I am trying to calculate the RMSD value of a single residue between two structures whereas the two structures should not get aligned on the single residue but the structures as a whole. Here is what I do so far:

parm WT.prmtop
trajin WT.inpcrd
parm ../../../../1d7p_data/crystal_structure/WT/WT.prmtop [1d7p]
rmsd :1-156&!.H= :4-159&!.H= reftraj ../../../../1d7p_data/crystal_structure/WT/WT.inpcrd parm [1d7p]
rmsd :25&!.H= :28&!.H= out 1iqd_to_1d7p_rmsd_2198.agr nofit reftraj ../../../../1d7p_data/crystal_structure/WT/WT.inpcrd parm [1d7p]

Is this the right way to do it?

Kind regards,
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Received on Mon Feb 04 2019 - 07:00:03 PST
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