[gmx-users] g_hbond

[Steven Neumann]

On Wed, Aug 31, 2011 at 3:44 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>>
>>
>> On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Steven Neumann wrote:
>>
>>        Hi Gromacs Users,
>>         I have calculated hydrogen bonds and collisions between my
>>        ligands and every single residue using g_hbond. Looking at the
>>        criteria adpoted by Gromacs I found impossible that number of
>>        hydrogen bonds were higher than number of collisions... And what
>>        is interesting in one of my residue I obtained result like
>>        this... All Hbonds with Glycine - 1872, All Collisions 704.
>>         Does anyone know how is it possible?
>>
>>
>>    I don't know how any of your numbers are possible (1872 H-bonds
>>    forming with a glycine?), or what you are defining as a collision
>>    and how you calculated it. Please provide the exact commands that
>>    you're using.  If you're equating a contact (e.g. from g_mindist)
>>    with a collision, then realize that the default criteria for a
>>    contact are very different than the geometric criteria for a
>>    hydrogen bond.
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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>>
>>  My system is made of 10 ligands and one protein. I used command:
>>  g_hbond -f md.trr -s md.tpr -n res91.ndx -num 91with10LIGbonds.xvg
>>  Where I specified in the index file two groups: 10 ligands and Glycine
>> residue. So I have calculated hbonds (second column) and collisions (third
>> column) and then I made a sum of all frames during 100 ns simualtion time
>> (one frame every 50 ps) obtaining 1872 hbonds and 703 collisions between
>> Glycine and 10 ligands. I did it with every residue to assess binding
>> affinity of different amino acids.
>>
>
> I forgot to mention in the previous message that there is no value in
> summing the hydrogen bonds over time.  Some of those H-bonds may be
> distinct, and others may be the same H-bond that has broken and subsequently
> re-formed.  I doubt anyone would find real value in saying that 10 ligands
> formed 1872 H-bonds with glycine over a trajectory.
>
> -Justin
>
> Obviosuly, but it can provide you some information about binding affinity -
some ligands remains close to some residues longer than the others so by sum
of this values you can assess residues with higher binding affinity.

Steven

>
> Criteria for collision is distance <3.5 A, and fo hbond distance <3.5 A and
>> angle. So when calcualting hbond and collisions the number of hbonds has has
>> to be smaller while collision takes into account hbonds as welll. I obtained
>> results like this for all other residues which seems to be correct. Am I
>> right?  Steven
>>
>>
>  --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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