[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
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."
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
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