[AMBER] ligand clustering

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Thu, 2 Jan 2020 15:47:51 +1000

Dear List,

I have a system consisting of ligand, protein, solvent and ions. The ligand
is initially positioned randomly in the solvent. I am interested in
performing cluster analysis in order to identify the pocket (maybe
transient) for the ligand of my interest. Here is my script

trajin trajout.nc (trajectory without ions and solvent)
rms first :1-176.C,CA,N,O (residues of the protein)
#rms first :LIG
cluster C0 out cnumvtime.dat summary summary.dat info info.dat rms mass
nofit :LIG clusters 10 clusterout cluster clusterfmt netcdf repout
representative repfmt pdb sieve 10

Could you confirm if the script makes sense for my objectives?


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Received on Wed Jan 01 2020 - 22:00:01 PST
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