Re: [AMBER] Distance between nucleotides and amino acids

From: Daniel Roe <>
Date: Mon, 3 May 2021 09:11:58 -0400


You could probably do this with a combination of 'for' loops and the
'avg' analysis. Something like:

parm tz2.parm7
for residues R1 inmask <protein mask>
  for residues R2 inmask <nucleic mask>
    distance d$$R2 out distances.dat $R1 $R2
avg d* out avg.dat name AVG

See the manual for full details. Pay attention to the output so you
can see exactly what is being done. I recommend trying on a small
subset of your trajectory first to ensure it's calculating what you

Hope this helps,


On Mon, May 3, 2021 at 6:20 AM Airy Sanjeev <> wrote:
> Dear Amber Users,
> I need to find out the distances between the nucleotides and amino acids
> from the pdb snapshots at an interval of 10 ps and then calculate the
> average distances with the standard deviation using cpptraj. Please suggest
> any useful.
> Thanks in advance
> --
> with best regards,
> Airy Sanjeev, PhD
> Post Doctoral Fellow
> Indian Institute of Technology Guwahati, Guwahati
> Assam-781039, India
> _______________________________________________
> AMBER mailing list

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Received on Mon May 03 2021 - 06:30:04 PDT
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