From: Rui Chen <rchen6.ualberta.ca>
Date: Mon, 13 Jan 2020 08:49:11 -0700


I am using CPPTRAJ to analyze the Hbonds and I have the following questions:
There are waters, ions, glycans, protein and a small-molecule inhibitor in
my system. I am using the following command "hbond All out All.hbvtime.dat
solventdonor :WAT solventacceptor:WAT.O avgout All.UU.avg.dat solvout
All.UV.avg.dat bridgeout All.bridge.avg.dat" according to a tutorial.
1. Should I specify the protein/ligand mask by using "hbond :1-432,433" and
add "nointramol" at the end of the command?
2. Residues 417 to 432 are glycans, do I need to include them in the
3. Is it correct to analyze all the solvent H-bond interactions (There are
more than 30,000 water atoms in my system) or specify important waters
(i.g. within 10 angstrom of protein and ligand)? What do researchers
usually do?
4. Then how to specify waters within 10 angstrom of protein and ligand?

Looking forward to your reply.

Best regards,
AMBER mailing list
Received on Mon Jan 13 2020 - 08:00:02 PST
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