Date: Sun, 30 May 2021 15:38:54 -0400
Dear AMBER Users
I have an inhibitor-bound complex, I want to study the ligand transition
states through umbrella sampling, attachment-pul-release approach. In APR,
we pull the guest gradually away from the host by imposing external
restraint, generating different RC/CV, and then those RC/CV run in
different windows.
My question is if during pulling guest make clash with side-chain atoms of
residue, (or we have we less space within the pocket to pull ligand away)
then how can we apply the umbrella or APR approach. I am also attaching the
image of my complex in which you can see that two F residues rings are at a
distance of 4.3A. NOw If I pull this guest away its adenine ring may cause
a clash with the phenylalanine side chain.
Looking forward to hearing from you.
Best
Rehan
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