Steven Neumann wrote:
On Wed, Aug 31, 2011 at 3:44 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.
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
Obviosuly, but it can provide you some information about binding
affinity - some ligands remains close to some residues longer than the
others so by sum of this values you can assess residues with higher
binding affinity.
The average number of hydrogen bonds over time will tell you the same thing,
with much greater precision. There are a maximum number of H-bonds that glycine
can participate in, since it only has backbone groups to contribute, so if you
find that, on average, there are 2.5 out of a possible 3 H-bonding sites
occupied, then yes, it is a strong interaction. Using some non-physical metric
will probably get you in trouble with reviewers. It's up to you to justify what
you're doing, but summing potentially redundant information doesn't make sense
to me.
-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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