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

[Liu Ji]

Hi Justin,

It seems that pdb2gmx determines the hydrogen position based on the
start structure. In this case, hydrogens are added for an optimal
hydrogen bond network. However, I am still wondering whether this for
one-conformation optimized hydrogen position will be inappropriate for
the rest of protein conformations.

Actually, I noticed a questionable hydrogen assignment in the
catalytic His residue of the enzyme, and yes, I can correct this if
related references are available. But for others, I'm not sure they
could be in correct state and how largely the hydrogen position will
affect the structure dynamics. Maybe I should compare the MD
trajectories from two different assignments and figure out this
problem. Anyway, thank  for your precious help.

Best wishes

Liu Ji
Institute of Bioengineering
Zhejiang University, China

On 7/16/09, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>>
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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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