AMBER Archive (2009)

Subject: Re: [AMBER] NOE

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Jun 11 2009 - 12:29:06 CDT

On Thu, Jun 11, 2009, Beale, John wrote:

> Is it possible to use NOESY or ROESY volume integrals as an input for
> sander? Is there a tutorial that explores this?

Chapter 6 of the Users' Manual is titled "NMR and X-ray refinement using
SANDER", and section is entitled "NOESY volume restraints"; section 6.7.1
illustrates how to prepare input (see especially the "-vol" and "-svf"
flags; section 6.11 has some sample input files.

Tutorial A4 goes over NMR refinement in general, although not with volume
restraints.

These are advanced options, and you will have to experiment some; but finding
the basic answers to your questions should have required no more effort than
perusing the Table of Contents.

...dac

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