[gmx-users] How does pdb2gmx assign protonation in default condition?

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 16 13:12:34 CEST 2009

Liu Ji wrote:
> Hi all,
> I have a question about how pdb2gmx determines the protonation of the 
> His residue in default. To best of my knowledge, His usually has its ND1 
> nitrogen free in un-protonated state, which might equal to the HISB 
> presents in pdb2gmx. However, when I am treating pdb files by pdb2gmx 
> without specifing exact state of His, the resulting structure contains 
> both HISA (NE2 free) and HISB (ND1 free) state as something listed below,
> There are 1155 hydrogen bonds
> Will use HISB for residue 151
> Will use HISB for residue 218
> Will use HISB for residue 368
> Will use HISA for residue 425
> Will use HISB for residue 449
> I am assuming that the hydrogen has been added in consideration of 
> steric interaction, however, does this assignment violate the common 
> knowledge? I can't find any references about this issue and am not sure 
> how large influence will be generated. So can you give me any 
> suggestions? Thanks a lot.

Quoting from pdb2gmx -h: "...for HIS the proton can be either on
ND1 (HISA), on NE2 (HISB) or on both (HISH). By default these selections are
done automatically. 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."


> Liu Ji
> Institute of Bioengineering
> Zhejiang University, China
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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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