[Chimera-users] addh question

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 10 14:40:14 PDT 2008

Hi Peter,
AddH (GUI or command) with the "consider H-bonds" option turned on  
does place hydrogens to fulfill hydrogen bonds for water as well as  
the protein, but it does not explore all the possible hydrogen- 
bonding network configurations to find some type of global optimum.   
Actually, I do not know if any method guarantees a global optimum,  
but various programs use different heuristics to narrow the search  
space.  We do suggest one alternative, somewhat more intensive  
method:  Reduce from the Richardson lab.  There is a link to this  
program and more information in the AddH man page:

You might want to try both approaches on a couple of test cases to  
decide what to use in your project, or delve into the literature to  
find additional programs.
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 10, 2008, at 2:22 PM, P. Law wrote:

> Hi,
>  	I am analyzing water-water and water-protein hydrogen bonds in a
> dataset of high resolution crystal structures. As part of this  
> analysis, I
> will need to add hydrogens to water molecules and to the protein.
>  	I was wondering how well the "addh" tool can place hydrogens on
> water molecules in the first shell around the protein?
>  	If addh is not the right tool for this task, are you aware of any
> freely available programs that can add hydrogens to 1st shell water  
> molecules
> in PDB files?
>  	Thanks for your help!
> Sincerely,
> Peter Law
> Graduate Student
> Biochemistry Department
> University of Washington

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