[gmx-users] electro-static potential energy after minimization
Jared James Thompson
thompsjj at purdue.edu
Tue May 4 16:54:30 CEST 2010
Do single-point MM/PBSA calculations. That's an energy value. But they may or
may not be accurate. "Energy values" as you put them are not simple and you may
need to run a simulation in order to obtain a proper ensemble. Such a
simulation is not for "refining the structure", it's to obtain an ensemble.
Then MM/PBSA or MM/GBSA may yield more accurate values of energy when you use
the ensemble of structures to perform these calculations.
Quoting abdullah ahmed <abdullah_renk_ahmed at hotmail.com>:
>
> The charged residues are on the inside of the structure, and so are not
> affected by the solvent. There are also no other charged residues in the
> structure. Furthermore, the structure is quite small 22 (residues). So I am
> still tempted to say that the coloumbic energy of the system should be
> affected by these charges.
>
> Regarding MD, the structure I am using is already in an optimal position. I
> am not particularly interested in refining the structure. All I really need
> is the energy value.
>
> > Date: Tue, 4 May 2010 08:53:48 -0400
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] electro-static potential energy after
> minimization
> >
> >
> >
> > abdullah ahmed wrote:
> > > Thank you for your reply,
> > >
> > > However, I can not use MD.
> > > I would simply like to ask whether I am correct in assuming that the
> > > minimized energies of the two structures should be very different.
> > >
> >
> > What exactly are you measuring? The Coulombic energy of the system? If
> so,
> > that term is going to be largely controlled by the solvent and thus you
> will see
> > little, if any, difference at all between the two systems. If you're
> measuring
> > the Coulombic energy between two residues, yes, you should see a clear
> difference.
> >
> > I don't understand your argument against MD. To me, restrained
> minimization
> > doesn't tell you much at all. But maybe I don't fully grasp your
> intentions for
> > these calculations.
> >
> > -Justin
> >
> > > > Date: Tue, 4 May 2010 08:41:15 -0400
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] electro-static potential energy after
> > > minimization
> > > >
> > > >
> > > >
> > > > abdullah ahmed wrote:
> > > > > Hello everyone,
> > > > >
> > > > > I have two protein structures, and the insides of both are not
> exposed
> > > > > to water.
> > > > > One structure contains two oppositely charges residues (GLU and
> LYS)
> > > > > facing each other. The second structure contains a GLU residue
> only.
> > > > > Upon minimization I had expected the coloumb energies of the first
> > > > > structure to be lower than that of the second. However, this was
> > > not the
> > > > > case, they are both very similar.
> > > > > Does anyone have an idea as to why this has happened?
> > > > > (The only explaination I can come up with is that perhaps the
> > > effect is
> > > > > so small that it can not be seen)
> > > > >
> > > >
> > > > We discussed this at length yesterday. By doing a simple energy
> > > minimization
> > > > (in which, if I recall, you are applying position restraints), you
> > > stand to
> > > > prove very little. By doing MD and obtaining an ensemble of energies,
>
> > > you stand
> > > > a better chance of calculating a relevant energy.
> > > >
> > > > > I was not sure if providing PDB and .mdp files would be helpful, but
> I
> > > > > can send then in my next mail if neccesary.
> > > > >
> > > >
> > > > The .pdb file is unnecessary. Only post the .mdp file if it has
> > > changed since
> > > > the one you posted yesterday.
> > > >
> > > > -Justin
> > > >
> > > > > Thank you in advance!
> > > > > Abdullah Ahmed
> > > > >
> > > > >
> > > ------------------------------------------------------------------------
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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 | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
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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 | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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--
Jared James Thompson
Department of Medicinal Chemistry and Molecular Pharmacology
Laboratory for Computational Drug Design and Biology
RHPH 504C
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