Steven Neumann wrote:
On Tue, Sep 6, 2011 at 3:09 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Tue, Sep 6, 2011 at 2:50 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au
<mailto:mark.abra...@anu.edu.au>>> wrote:
On 6/09/2011 11:37 PM, Steven Neumann wrote:
Dear Gromacs Users,
I am calculating hbonds between my 10 ligands and each
residue... How does Gromacs calculate average number of
hbonds
per timeframe?
Example:
for Glycine:
Av. num of hbonds/timeframe
0.96
To check whether that is correct I added all hbonds
formed with
Glycine during my simulation time over 2000 (each 50ps)
timeframes and I obtained value: 2900. If you divide it
by 2000
you will never get 0.96 obviously. How does Gromacs
calculate it?
Presumably by adding up the number in each time frame and
dividing
by the number. Unless you have a highly-exposed glycine, forming
more than one H-bond seems unlikely, and your 2900 number
suggests
it's happening lots of times. I expect you're comparing a sum of
oranges with a sum of apples, but without more information about
what you're doing in your attempt to check, we can't help much.
Please be sure to read g_hbond -h, and the legends of any
.xvg files
you're looking at.
Mark
Thank you Justin and Mark,
Yes, just found the mistake... I added pairs within 3.5 A
instead of hbonds so the Gromacs calculation is correct. So the
value is 0.96 for Glycine. So in this case it is a strong
interaction. Are there any criteria to assess strenght of
interactions or binding affinity for residues? Was it described
anywhere for each residue to specify these values with respect
to possible hbonds for each residue (e.g. Glycine - 3)?
Binding affinity can be determined from free energy calculations,
but for the case of multiple ligands this would be an incredibly
complex calculation (or series of calculations, really). You might
be able to make some argument about occupancy of available hydrogen
bonding sites.
-Justin
So will it be possible to exteract one ligand which from my
visualisation occupy one residue with highest number of av. hbonds
(others aggregate on bounded or bind weaker) and then calculate free energy?
Something like that might be possible, by calculating free energies over an MD
rerun, but I've never tried it so I won't speculate. Consult the literature for
precedent and procedure and have a look at the free energy tutorial on the
Gromacs site to see if you can piece it all together. It won't be a trivial
exercise.
-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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