Re: [AMBER] NOESY volumes restraints

From: David A Case <>
Date: Mon, 13 Jul 2015 07:50:01 -0400

On Fri, Jul 10, 2015, Eugene Sviridov wrote:

> - Since my molecule isn't very big (630 atoms, see attachment), would it be
> better to use only one submolecule (entire molecule)?

You could probably do that. I haven't run these sorts of calculations in more
than 10 years, so my memory of details may be rather limited.

> - The molecule structure changes during the MD run so do the calculated
> values of volumes. Should I periodically change oscale to maintain the
> calculated and measured intensities at the same level?

I'd think this would only be necessary if the structure changed a lot during
refinement. I only used NOESY restraints once I had a good initial structure.

> - If I keep default value of the NOESY weight (=1) the NOESY energy (~30)
> is much less then EAMBER (~-5000), so NOESY restraints seem to have no
> influence on the simulation. What value of NMR volumes restraints energy is
> appropriate for minimization/MD/annealing at T=300K? Should it be
> comparable with the dihedral angles energy, for instance?

The absolute value of the Amber energy is not relevant here, since its zero
is arbitrary. You will probably have to experiment some to find a NOESY
weight that is good for your system.

> - I want to use values of Pearson r, Rms error, R1 and Rr as criteria of
> whether the structure is in agreement with experimental data, but there are
> not a lot of works with NOESY volumes restraints, so could you tell what
> values of these factors are considered as appropriate for nucleic acid
> simulations?

I don't know the answer here: one good question to ask is whether the
structure changes much on moving from more conventional distance restraints to
volume ones.


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Received on Mon Jul 13 2015 - 05:00:03 PDT
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