Re: [AMBER] NOESY volumes restraints

From: David A Case <>
Date: Mon, 6 Jul 2015 08:42:02 -0600

On Mon, Jul 06, 2015, Eugene Sviridov wrote:
> I'm trying to solve DNA-duplex structure using MD with NOESY volumes as
> restraints.
> When I try to minimize the structure it looks like the molecule doesn't
> feel any restraints: I tried to increase restraints weights, to use random
> volumes values and no volumes restraints at all - resulting structures are
> nearly the same (<0.5 RMSD).

We would need lots more information to be of much help. You should be able to
see from the mdout file whether you have NOESY penalties being applied or not.
In particular, you can see whether or not the calculated and measured
intensities are close to each other, etc.

There are example files in $AMBERHOME/test/noesy that you can compare to what
you are getting. But, as a beginner, you should certainly run NMR restraint
calculations with "conventional" restraints (as in Tutorial A4) before trying
NOESY volume restraints (which is most definitely a very advanced
> Could it be connected with a wrong value of "oscale" parameter? I failed
> to find any information about its determination. How could I estimate it?

Pick some intense peaks whose assignments are clear, and determine oscale such
that the calculated and measured intensities become as close as they can.


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Received on Mon Jul 06 2015 - 08:00:02 PDT
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