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

From: Daniel Roe <>
Date: Mon, 4 Feb 2019 13:26:14 -0500


This seems ok, except if WT.inpcrd is a single structure you're
probably better off loading it as a reference, e.g.

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


On Mon, Feb 4, 2019 at 9:33 AM Rosellen, Martin
<> wrote:
> 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]
> go
> Is this the right way to do it?
> Kind regards,
> Martin
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Received on Mon Feb 04 2019 - 10:30:03 PST
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