[phenixbb] Problems fitting NADH

Nathaniel Echols nechols at lbl.gov
Fri Mar 30 13:21:11 PDT 2012

On Fri, Mar 30, 2012 at 1:14 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,

What did you use as input for eLBOW?  Assuming the ligand geometry
output by LigandFit is okay, you might want to include this as input
to eLBOW as the final geometry, along with NAI as the chemical
components code.


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