AMBER Archive (2008)

Subject: AMBER: MD with NMR restraints

From: Sally Pias (sallypias_at_gmail.com)
Date: Wed Aug 13 2008 - 23:25:56 CDT

Hello all,

I have a medium resolution NMR structure from which I am attempting to
run explicit solvent molecular dynamics simulations. The structure is
unstable if no NMR restraints are applied during the simulations, so I
have carried out a lengthy production run (20 ns) using NOE-based NMR
restraints. My question is whether this sort of restrained simulation
is "useful," in terms of providing credible information about loop
dynamics. If the structure is unstable without restraints, should I
be concerned that the data collected with restraints are contrived? I
am attempting to correlate data from the MD simulations with
experimental observables, such as B-factors and NMR relaxation data.
However, I wonder if I am headed down a path that will leave me with
data whose value cannot be substantiated (because of the restraints).
Are there examples in the literature of MD simulations carried out
with NMR restraints?

Thanks for your help.

Sally Pias
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu