[gmx-users] the different protonation state of HIS

Peter C. Lai pcl at uab.edu
Thu Apr 5 15:28:14 CEST 2012

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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