[Chimera-users] Minimize

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 4 10:54:56 PDT 2009

Hi Alex,
I  would not worry, just use the "also consider H-bonds" method when  
adding hydrogens in Chimera.  That method is the default.

In fact hydrogens might be totally irrelevant to DelPhi depending on  
what DelPhi parameter files you are using.  If I recall correctly,  
their "default.crg" and "default.siz" files are for use on structures  
without hydrogens.   By far the most difficult thing is making sure  
parameters are assigned correctly and that the net charge of your  
protein in the delphi log file is what you expect.  Sometimes people  
use parameter files with hydrogen names that don't match those in the  
structure and the net charge of the protein is reported in the log  
file as a huge negative non-integer.

Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 4, 2009, at 10:21 AM, Alex Gawronski wrote:

> Thanks for the info!
> I was just worried that the added hydrogen atoms would not be in the  
> minimal position. They do move a little from the minimization. Do  
> you think that is significant?
> Alex Gawronski

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