Dear AMBER users,
I am trying to compute the average water population in the protein-ligand
binding site. I am using "watershell" cpptraj for that. My cpptraj.in file
is as follows:
"parm com-solv.prmtop
trajin traj.nc
watershell "solutemask (protein-ligand complex residue range)" lower 3.4
noimage "solventmask (residue range of water)".
My question is:
1. Should I have to provide only the protein-ligand active site residue
range ya watershell will automatically search and find that ?
2. Secondly, should I have to provide both explicitly lower and upper
cutoff while doing the calculations?
Your suggestions would be highly appreciated.
Thanks & Regards
Kankana Bhattacharjee
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Received on Tue Sep 26 2023 - 06:00:02 PDT
