[AMBER] conformational sampling for organic/drug-like compounds

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Wed, 10 Jul 2019 19:16:12 +0100

Dear All,
I am assuming that performing standard gas phase or explicit water MD
simulations on drug-like organic compounds would not sample all possible
conformations especially when TS for some torsional transitions is expected
to be higher than 5-10 kcal/mol. Some compounds may have up to 10
rotatable bonds.
Thus can you please suggest which approach would be best for doing this in
Amber19?
1) Perform external conformational sampling and do separate MD simulations
with a selected set of low energy conformers.
2) Simulated annealing type MD to sample conformations within Amber and
then possibly choose lowest energy conformers to perform
unconstrained/unguided MD.
3) something very different (that I'm unaware of)?
The idea is to compare/analyze conformational freedom that these compounds
have in solution and within protein active sites.
Thank you and best regards.

-- 
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
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Received on Wed Jul 10 2019 - 11:30:03 PDT