[Chimera-users] addh question

[Elaine Meng]

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:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html

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
-----
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
                       http://www.cgl.ucsf.edu/home/meng/index.html

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
>