[gmx-users] g_hbond

Wed Aug 31 17:25:21 CEST 2011

Thank you for clarification Justin!!! The Manual is not as clear as you :P

Steven

On Wed, Aug 31, 2011 at 4:00 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>>
>>
>> On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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>
>>         <mailto: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/> <http://vt.edu/> | (540)
>>
>>        231-9080 <tel:%28540%29%20231-9080>
>>           <tel:%28540%29%20231-9080>
>>
>>           http://www.bevanlab.biochem.
>>        <http://www.bevanlab.biochem./**>____vt.edu/Pages/Personal/**
>> justin <http://vt.edu/Pages/Personal/justin>
>>        <http://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<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.
>>        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?
>>
>>    No.  The second column is not inclusive of the first.  It counts the
>>    number of atoms that are within hydrogen bonding distance, but do
>>    not meet the criteria because of the angle between D-H-A.
>>
>>
>>    -Justin
>>
>>    In this case number of collisions has to include number of hbonds.
>>    If collision is counted as a distance <3.5 and hbond distance <3.5
>>    plus angle D-H-A means that collisions covers hbonds... Explain
>>    please whether I am wrong.
>>
>>
> The second column lists the number of atom pairs that satisfy the distance
> requirement but do not satisfy the angle requirement and therefore are not
> hydrogen bonds.  The two columns are mutually exclusive.  The sum of these
> two columns would be the total number of pairs that are within
> hydrogen-bonding distance, but the first column indicates those that are
> actually involved in hydrogen bonds (because of the angle), and the second
> column indicates those that are not involved in hydrogen bonds.
>
>
> -Justin
>
> --
> ==============================**==========
>
> 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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