Steven Neumann wrote:
On Wed, Aug 31, 2011 at 3:38 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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://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
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