Hi all,<br><br>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,<br>
<br>There are 1155 hydrogen bonds<br>Will use HISB for residue 151<br>Will use HISB for residue 218<br>Will use HISB for residue 368<br>Will use HISA for residue 425<br>Will use HISB for residue 449<br> <br>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.<br>
<br><br>Liu Ji<br>Institute of Bioengineering<br>Zhejiang University, China<br>