[Chimera-users] Add-H to water O

Elaine Meng meng at cgl.ucsf.edu
Wed May 9 10:25:15 PDT 2012

Hi Francesco,
While Chimera AddH does pay attention to local H-bonding, it will not go through extended networks to find an optimum pattern of hydrogen addition. Also, AddH always adds hydrogens to the whole model (although you can certainly delete some of them after that).  

Assuming your protein structure already includes the water oxygens, you may want to try first adding hydrogens, then minimizing (Tools... Structure Editing... Minimize Structure) but only allowing the waters to move.  If your protein does not already have waters, you could add hydrogens, then use the Solvate tool (also under Tools... Structure Editing), then possibly minimize waters only.

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

On May 9, 2012, at 9:14 AM, Francesco Pietra wrote:

> Is it possible with CHIMERA to add-H selectively to O atoms to get
> H-bonded water molecules?
> I used REDUCE to add-H (-build flag) but was unable to get H2O from O
> atoms, although het database is in place.
> What I am trying to get is a reasonable H-bonded water for a highly
> hydrated protein, before submitting to MD to actually see h-bonding.
> thanks
> francesco pietra

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