Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> 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://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
--
========================================
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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