Steven Neumann wrote:
On Wed, Aug 31, 2011 at 2:39 PM, Justin A. Lemkul <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/> | (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.
I forgot to mention in the previous message that there is no value in summing
the hydrogen bonds over time. Some of those H-bonds may be distinct, and others
may be the same H-bond that has broken and subsequently re-formed. I doubt
anyone would find real value in saying that 10 ligands formed 1872 H-bonds with
glycine over a trajectory.
-Justin
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?
Steven
--
========================================
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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