Dear Amber Users
I modified some already known inhibitors, Now I want to calculate binding
free energy of each residue with respect to inhibitor, But I do not want
the surrounding residues to contribute to the energy of a particular
residue which is interacting with the ligand. As I know, we can perform
per-residue decomposition analysis in amber but in this analysis we can get
each residue decomposition energy but this energy also has the contribution
of surrounding residue. Please correct me if i am wrong. Also guide me how
I can calculate energy contribution of a particular residue towards ligand
without considering surrounding residue impact on that particular residue.
Looking forward to hearing from you.
Best wishes
Rehan
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Received on Mon May 24 2021 - 10:30:02 PDT
