AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: David A. Case (case_at_scripps.edu)
Date: Thu Jan 24 2008 - 20:18:48 CST

On Thu, Jan 24, 2008, Seth Lilavivat wrote:
>
> In the NMR refinement tutorial, it suggests setting ialtd=1 if your
> structure is distorted due to an opposition of restraints and force field.
> Is it ok to refine the structure using the ialtd=1 or is this meant as a way
> to help find bad restraints?
>

You can do refinements with ialtd=1, but you would want to look carefully at
any large NOE violations that are encountered, and figure out if you can live
with them or not. Sometimes a "soft" restraint like this will end up throwing
out important information.

...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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