AMBER Archive (2008)

Subject: Re: AMBER: MD with NMR restraints

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Aug 20 2008 - 12:07:15 CDT

On Wed, Aug 13, 2008, Sally Pias wrote:
>
> 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?

Your instincts are correct: you should be suspicious of structures that
are "unstable" without restraints. But without knowing more about your
particular problem, it's hard to say more: the problem could be with the
force field itself, or it could be with the starting (NMR) structure, or
something else....

...good luck...dac

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