From: manish kesherwani (
Date: Wed Apr 16 2014 - 13:21:34 CDT

Sorry for my confusing written english.

I need to calculate binding free energy for membrane protein-ligand complex.

>From literature binding free energy

 delta Gtotal = delta Gelc + delta Gnp + delta Glip + delta Gimm + delta

I can easily calculate solvation energy part by using MMGBIM module of
charmm (Gele+Gnp) using ensemble of protein-ligand complex conformation
by removing atoms belong POPC lipid and TIP3P water from 50ns simulated

How we can calculate Glip( lipid perturbation effect) ,Gimm( immobilization
effect) and Gcon ( conformational effect) term for determining free energy.

Thanks for reply and giving me suggestion.
Thanks & Regards
Manish Kesherwani

On Tue, Apr 15, 2014 at 11:47 AM, Aron Broom <> wrote:

> In general, it seems from the wording of your question that maybe you are
> missing a lot of basic information concerning thermodynamics, and your line
> of questioning may change a lot by spending some time learning some of
> those fundamentals.
> In particular, computing the free energy an entire system, and then
> deleting a portion of it and recalculating, is in many cases, nearly
> meaningless. You've not just reorganized the system (which would be
> meaningful) but actually made a different system, and are now comparing two
> different things. But maybe that wasn't where you were headed. At any
> rate, brushing up on the basics might allow you to formulate a less vague
> or confusing question.
> On Tue, Apr 15, 2014 at 1:14 PM, Kenno Vanommeslaeghe <
>> wrote:
>> We saw your post the first time. If you didn't get a reply, then maybe
>> you should think whether there's a problem with your question instead of
>> posting almost the same thing again.
>> On 04/15/2014 01:02 AM, manish kesherwani wrote:
>>> Respected Sir,
>>> I am Manish Kesherwani Phd student under Prof D.
>>> Velmurugan University of Madras India. I simulated transporter channel
>>> using namd from charmmgui prepared script. I observed changes in rmsd of
>>> protein till 3 Ang during 15ns equilibration NVT followd by NPT. I
>>> talked to Dr sunhwan charmmgui developer they told us protein can
>>> fluctate due to 4 Ang low resolution structure. Then 50 ns production run
>>> was carried out.
>>> I am interested to calculate gas phase energy of protein for
>>> calculating free energy. I observed total system potential energy is
>>> negative. I extracted the protein conformation from solvated trajactory
>>> by
>>> removing water and lipid and calculated the energy of protein. it shows
>>> positive. I understand the protein is unstable but i am not able to take
>>> any reasonable conclusion.
>>> Please give some suggestion. I will be highly obiliged.
>>> Thanks & Regards
>>> Manish Kesherwani
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

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