[AMBER] Stripping waters from trajectory except those forming bridged H-bond between Protein and Ligand

From: Rakesh Srivastava <allahabad.21.gmail.com>
Date: Sat, 12 Mar 2022 10:42:50 +0530

Dear Amber users, for a MMPBSA calculation, I want those explicit water
molecules to be kept in the trajectory which form a bridged H-bond between
protein and ligand, while the rest of other water molecules to be stripped.
I am looking for a way to perform this using cpptraj but not getting
success. Could anyone please help me how to carry out this?
Thanks in advance.

*Rakesh Srivastava, Ph.D.*
Postdoctoral Fellow
Center for Computational Natural Sciences and Bioinformatics (CCNSB)
International Institute of Information Technology, Hyderabad, India
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Received on Fri Mar 11 2022 - 21:30:02 PST
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