Re: [phenixbb] Problems fitting NADH

Phillip Problems with non-tetrahedral phosphates can sometimes mean that the starting geometry for the oxygens on the phosphates are switched. You can check on possible problems in the .geo file. Look in the angle and dihedral sections for large residuals. I have attached a restraints file from the most recent version of eLBOW in case that helps. I used phenix.elbow --chemical-components=nai If you still have trouble send me the files directly so I can investigate. Nigel NB. Any files sent to me will be held in strictest confidence. On Fri, Mar 30, 2012 at 1:21 PM, Nathaniel Echols wrote:

On Fri, Mar 30, 2012 at 1:14 PM, Phillip Steindel 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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