Hi,
You could probably do this with a combination of 'for' loops and the
'avg' analysis. Something like:
parm tz2.parm7
trajin tz2.nc
for residues R1 inmask <protein mask>
for residues R2 inmask <nucleic mask>
distance d$R1.to.$R2 out distances.dat $R1 $R2
done
done
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
want.
Hope this helps,
-Dan
On Mon, May 3, 2021 at 6:20 AM Airy Sanjeev <airy.sanjeev01.gmail.com> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 03 2021 - 06:30:04 PDT
