On 2012-04-05 06:19:07AM -0700, Acoot Brett wrote:
> Dear All,
>  
> For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS 
> format at pH 7?

-ignh does not do what you think it does. -ignh ignores the original PDB's 
hydrogen coordinates.

Picking the "correct" histidine protonation at pH 7 is still structure-
dependent since either nitrogen can be protonated.

The manual for pdb2gmx states the following automatic HIS protonation:
"For His, this is based on an optimal hydrogen bonding conformation. 
Hydrogen bonds are defined based on a simple geometric criterium, 
specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor 
distance, which are set by -angle and -dist respectively."

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Peter C. Lai                    | University of Alabama-Birmingham
Programmer/Analyst              | KAUL 752A
Genetics, Div. of Research      | 705 South 20th Street
p...@uab.edu                    | Birmingham AL 35294-4461
(205) 690-0808                  |
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