[gmx-users] g_hbond
Steven Neumann
s.neumann08 at gmail.com
Wed Aug 31 17:49:13 CEST 2011
One question.... for Glycine it is easy to assess 3 possible hbonds which
can create as hydrogen is only one atom as a side chain.
How about other amino acids and their maximum hbonds they can create?
Steven
On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:
> 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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