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

Liu Ji zjuliuji at gmail.com
Thu Jul 16 07:24:07 CEST 2009

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

Liu Ji
Institute of Bioengineering
Zhejiang University, China
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