[phenixbb] Problems fitting NADH

Shya Biswas shyabiswas at gmail.com
Fri Mar 30 13:42:31 PDT 2012

Hi Phillip,
You have to check your ligand geometries in reel, and do modifications
accordingly of your pdb file. Sometimes the submitted pdb files in the
database does not have right bonds. Alternatively try generating your
restraints using smilestrings instead of pdb it always works better.

On Fri, Mar 30, 2012 at 4:14 PM, Phillip Steindel <pstein at brandeis.edu>wrote:

> Dear all,
> I'm trying to fit a NADH into a 1.7 Å structure.  LigandFit worked with
> just the three-letter code (NAI), however phenix.refine won't work with
> just the model. If I use eLBOW to create restraints, meanwhile, the ligand
> gets distorted during refinement (non-tetrahedral phosphates, mainly).  I'm
> not sure exactly how I'm supposed to be generating these restraints- any
> help is appreciated.  Thank you,
> Phillip Steindel
> Theobald Lab
> Department of Biochemistry
> Brandeis University
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