Anirban Ghosh wrote:
Thanks a lot Justin for the reply !!!
While calculating the Elj and Eqq values should we consider the
short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in
1-4 interactions are intramolecular, thus should not be relevant to the LIE
calculation.
the .edr file? And for Coulomb also?
Which one should we consider?
Did you use PME? If so, you can't break down the Coulombic terms entirely.
-Justin
Thanks again.
Anirban
On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
Yes I am going through all the relevant literature on LIE.
Actually the lie.xvg file contains the same value of -25.4 for
all the frames. So I am getting a straight line plot. Why is
this happening? Am I missing out something?
If the interactions of your ligand and its receptor are stable, then
there may be no change in the energetics. I don't know anything
about your system, so I can't say anything beyond that.
-Justin
Thanks a lot again.
Anirban
On Tue, Dec 28, 2010 at 6:24 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
So I ran a simulation with my ligand in water for 1 ns
and using
g_energy I calculated the LG-14 and Coulomb-14 values
from the
.edr file. I supplied the average of these two values as
my Elj
and Eqq to g_lie and I got the DGbind as -25.4. Is this the
correct way to do this?
Again I would ask you to not rely entirely upon my advice for
this.
I have only examined the LIE method sparingly. My best
answer is,
"probably," but do read the literature on the method to be sure.
And why am I getting only a single value of DGbind for
all the
frames captured in the .edr file?
The lie.xvg file contains the LIE values as a function of time.
What's printed to the screen is the average value and standard
deviation.
-Justin
Thanks a lot.
Anirban
On Mon, Dec 27, 2010 at 11:51 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:
Anirban Ghosh wrote:
Thanks Justin for the reply.
I have through the threads about g_lie, but cannot
understand
how to get the values for Elj and Eqq for a particular
ligand.
Like in my case for a system consisting of a beta2AR
protein +
dopamine (ligand) + POPC + water, what should be the
values for
Elj and Eqq?
To obtain these (from my limited understanding), you would
have to
run a simulation of your ligand in water, decomposing the
nonbonded
energies between the ligand and solvent into LJ and
Coulombic
components. Those are your values.
I should also note that simply going through the
archive to
inform
yourself about the LIE method is insufficient. The
original
literature, and several subsequent papers (one at least
within the
last year, IIRC), describes the accuracy of the method and
what it
needs to be properly run.
-Justin
Thanks a lot.
Anirban
On Sat, Jul 17, 2010 at 4:56 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>> wrote:
Anirban Ghosh wrote:
Hi ALL,
I have run a protein + ligand (dopamine)
simulation. Now
I want
to calculate the free energy of binding using
g_lie. But
g_lie
asks for two values: Elj and Eqq. How or from
where can I get
these values for my ligand? Also, do I need
to run a
simulation
with only the ligand? And, is there any
other way
(like
MMGBSA
in Amber) to calculate the free energy for my
simulation? Any
suggestion is welcome.
Thanks a lot in advance.
Go to the literature and understand what
information is
needed for
such a simulation, and then look into the list
archives and
you'll
find dozens of threads about using g_lie.
-Justin
Regards,
Anirban
-- ========================================
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>
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-- ========================================
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>
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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ICTAS Doctoral Scholar
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Virginia Tech
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