[gmx-users] histidine charges

[Anton Feenstra]

Aswin Narain wrote:
> hi all,
> I was just wondering how the protonation states of Histidines are 
> assigned by gromacs? For some histidines with low solvent 
> accessibility (found by means of WHATIF) the Histidines are 
> assigned a protonation state of HISB (accessibility is less than 
> 2.0) but for an accessibility of 24.9014 the histidine is assigned 
> a state HISB and for an accessibility of 19.305 the histidine is 
> assigned a state HISA then a histidine with accessibility 4.1372 
> the state assigned is HISH by gromacs  on what basis is the 
> assignments made as I am trying to do some pH based MD work??

pdb2gmx determines (guesses) at protonation state by examining
possible hydrogen bonding partners. I'm not sure how much it
actually prints out about it's decisions. Non-accessible residues
will be (almost) completely determined by the possible H-bonding
partners, also interior but accessible residues can be influenced
greatly by their surrounding, and only accessible ones depend wholly
on solvent pH.

There was some extended discussion on the list on pH-MD a week or so ago.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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