[gmx-users] Further question on protonation state of histiding

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 6 12:45:24 CEST 2012

Acoot Brett wrote:
> Dear All, 
> For low resolution structure PDB, the protonation state of histidine is 
> niot clear. Then how does pdb2gmx treat the protonation state of HS?
> Even for high resolution structure of protein, the protonation state of 
> HIS is usallly unclear or unspefified.
> In the manual og gromacs, although it involves different protonation 
> state of HIS (and some other residues), but the whole manual never 
> request us to modify the PDB file for pdb2gmx input.
> Thus can we consider pdb2gmx process the protonation state of residues 
> (including HIS) automatically?

I answered this yesterday:


Please pay attention to advice you've already been given, or else people become 
less likely to give it.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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