[gmx-users] on PDB2gmx

Peter C. Lai pcl at uab.edu
Sat Apr 7 03:58:43 CEST 2012

On 2012-04-06 06:41:57PM -0700, Acoot Brett wrote:
> Dear All,
> Can I remove all the H from the PDB file and then input it to the pdb2gmx so that pdb2gmx can produce all the correct protonation state of the protein residues including HIS?
> Cheers,
> Acoot   

It will not do what you expect. There is no "magical way" for pdb2gmx to  
determine HIS protonation. The best it can do is calculate potential H-bonding
and assign protons from there; and there is no guarantee it will be "correct"
or fit your expectations. You should really determine what criteria to choose
for histidine protonation state and assign them manually for best effect.

Justin already answered this question in a different way. Perhaps there is a
language barrier/problem involved?

Peter C. Lai			| University of Alabama-Birmingham
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