Re: what's the latest on using NAMD (and MD in general) for docking?

From: Homeo Morphism (homeo.morphizm_at_gmail.com)
Date: Thu Mar 21 2019 - 02:04:27 CDT

Thanks for this rather detailed explanation how it should properly be
approached, but I'm very new to MD and still curious as to why it can't be
used for this on a powerful workstation. Modern GPUs allow daily
simulations of trajectories as long as hundreds and hundreds of nanoseconds
for structures as large as dozens of thousands of atoms, don't they? Run it
for a week and you have microseconds. Isn't it enough for our particular
task? It's not like we need to explore the receptor's whole surface -- we
know with a very high degree of confidence where the original ligand docks
to the receptor. Just need to make somewhat sure that the bit that is
appended to the ligand can't stop it from docking in the very same area. So
if the modified ligand in any particular simulation starts drifting away
from the area of interest, you simply restart. If it drifts away always or
more often than not, then you discard it. Can't it work? Thanks, Oleg

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