Dear Amber users,
How can one calculate the binding mode entropy via normal mode
calculations on a truncated system in a way described, for example, in
the paper by Genheden et al
(
https://pubs.acs.org/doi/abs/10.1021/ci3001919)? Simply stripping the
unwanted part of the enzyme will probably result in a significant change
of geometry during the minimization of the snapshots. However, I can't
find a way to constrain residues when using the MMPBSA.py script (or
nmode for that matter).
Best regards,
Marko
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Received on Thu Aug 30 2018 - 08:30:02 PDT
