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."
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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