AMBER Archive (2007)

Subject: Re: AMBER: NMR violations increase in explicite water

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 15 2007 - 10:40:12 CST

On Wed, Feb 14, 2007, Michel Becker wrote:
>
>
> I am a little confused of the behaviour of my NMR-Refinement and it would be
> great if you could make any suggestions to my problem.
>
> At first I did a simulated annealing and a small Refinement in implicit
> solvent. The result was really satisfying ( I am simulating a DNA/drug
> complex and I know from circular dicroism experiments, that the DNA should
> look like a B-DNA in the drug/DNA complex as well) and the violation energie
> was approximatly 6 kcal/molAČ.
>
> After that I took the output geometries and carried about a NMR-refinement
> over 1 ns in a TIP3 waterbox. And the result is even better. The DNA looks
> now like a B-DNA nearly without any pertubations. And the force field
> shouldn't be overestimated because I set force constants for the
> NMR-restraints of 50 kcal/molAČand I have employed around 12 restraints per
> nukleotide. But the violation energy has mor than doubled (~14 kcal/molAČ).
>
> I really don't know how to interpret the result. Does I have to take it in
> account, that the refinement in implicit water ends at 0 K and the MD with
> NMR-Restraints in explicit water is carried out at 300 K? Or are this
> violation energies just not comparable?

I think you have it exactly right: the thermal fluctuations in the 300K
simulation will give on average a higher NMR constraint violation energy than
will a minimized struture, which will be close to the "bottom of the well".
So the average restraint energy (which is in units of kcal/mol, not
kcal/molAČ, by the way) will be higher.

...good luck...dac
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