[gmx-users] g_hbond
Steven Neumann
s.neumann08 at gmail.com
Thu Sep 1 10:14:46 CEST 2011
On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Steven Neumann wrote:
>
>> 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?
>>
>>
>
> Any OH or NH group is a donor, any lone pair is an acceptor (though
> obviously not modeled explicitly in MD). The ability of MD force fields to
> agree with reality in this respect is debatable, but should come close.
>
> -Justin
>
> Thank you Justin. Can you please clarify me something and tell me whether I
> am wrong. This is what I obtained from calulating hbonds between 10 ligands
> and Glycine. Each ligand serve 8 OH group (flavanoid) :
*Reading file md.tpr, VERSION 4.5.4 (single precision)
Specify 2 groups to analyze:
Group 0 ( r_96) has 7 elements -* this is my Glycine -
7 atoms (side chain - Hydrogen)
*Group 1 ( LIG) has 510 elements -* these are 10
ligands, 51 atoms each, 8 OH group
*Select a group: 0 1
Selected 0: 'r_96'
Select a group: Selected 1: 'LIG'
Checking for overlap in atoms between r_96 and LIG
Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms)
Found 81 donors and 112 acceptors *
**
*81 donors? It should be 80 when I have 10 ligands with 8 Oh group... Am I
right?*
*112 acceptors? 7 atoms of my Glycine x 12 possibilities?*
**
*trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Will do grid-seach on 11x11x11 grid, rcut=0.35
Last frame 2000 time 100000.000
Average number of hbonds per timeframe 0.642 out of 4536 possible - that
is understood = (112x81)/2*
**
*So how many possibilities has Glycine in order to create hbond? Shall I
choose just a side chain which is hydrogen?*
**
*Steven*
> Steven
>>
>>
>> On Wed, Aug 31, 2011 at 4:25 PM, Steven Neumann <s.neumann08 at gmail.com<mailto:
>> 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
>> <mailto: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>
>> <mailto: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>>
>> <mailto: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/> <http://vt.edu/> | (540)
>>
>> 231-9080 <tel:%28540%29%20231-9080>
>> <tel:%28540%29%20231-9080>
>>
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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 <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>
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> --
> ==============================**==========
>
> 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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