[gmx-users] Coul-SR: positive value for interating group
Mark Abraham
mark.j.abraham at gmail.com
Wed May 27 22:16:44 CEST 2015
Hi,
The present analysis says almost nothing about the interaction, neither
proof nor disproof. Along with what others have already said, stability is
relative to the available alternatives. You can start saying something
about stability associated with the arginine if you've e.g. measured the
free energy of binding with the arginine vs the free-energy of binding with
some similarly sized non-polar residue, for example. That is several orders
of magnitude more complex, however...
Mark
On Wed, 27 May 2015 17:18 Raj D <gromacs.for.f at gmail.com> wrote:
> Thank you once again Dr Andre... So to identify the true interaction
> partner for the ligand's Carboxlate in simulation ...may I have to define
> the energy group as all amino acids of protein vs the carboxlate group of
> the ligand or any easy way out ... Since from my trajectory visualization
> it seemed the Arg 262 is stabilizing the carboxylate of the ligand but the
> electrostatic interaction analysis disproved it .
> Regards,
> Raja
> On May 27, 2015 8:25 PM, "André Farias de Moura" <moura at ufscar.br> wrote:
>
> > I agree with Mark: pairwise additive potentials are computationally
> > convenient, but nature does not work like that.
> >
> > based on your email, it is seems that you are looking for an
> > energy/enthalpy term explaining some structural pattern, but in most
> cases
> > entropy role is also important and in some case might even be the leading
> > contribution. That being said, you should probably consider some sort of
> > PMF instead of looking for specific mechanical interactions.
> >
> > Andre
> >
> > On Wed, May 27, 2015 at 10:11 AM, Mark Abraham <mark.j.abraham at gmail.com
> >
> > wrote:
> >
> > > Hi,
> > >
> > > Indeed. Many force fields in common use are additive, but this is not
> the
> > > same as decomposable!
> > >
> > > Mark
> > >
> > > On Wed, May 27, 2015 at 2:52 PM André Farias de Moura <moura at ufscar.br
> >
> > > wrote:
> > >
> > > > Raja,
> > > > just guessing, based on the few informations you posted: if the local
> > > > dipole moments of these groups are parallel to each other,
> interaction
> > is
> > > > expected to be repulsive, even though they have opposite charges.
> Also
> > > mind
> > > > that overall structure in such complex systems depends on many
> > different
> > > > interactions, so these two groups are not necessarily close because
> > they
> > > > have interacted favorably, but because the overall interactions
> within
> > > the
> > > > whole system eventually led these groups to approach each other, just
> > > like
> > > > groups bearing the same charge pack together in micelles, membranes
> and
> > > > films, with large repulsive interactions between the charged heads
> > > > (stabilization comes from ionic and dipolar screening along with
> > > > hydrophobic interactions).
> > > > best
> > > > Andre
> > > >
> > > > On Wed, May 27, 2015 at 3:09 AM, Raj D <gromacs.for.f at gmail.com>
> > wrote:
> > > >
> > > > > Dear Users,
> > > > > I have just completed simulation of a ligand and enzyme complex and
> > > > > when I visualized the trajectory , I have noted an important close
> > > > > contact say about (7 to 10 A distances) between an active site
> > residue
> > > > > Arg and the carboxylate group of the ligand through out the
> > simulation
> > > > > time of 10ns. I wanted to quantify it using mdrun -rerun option and
> > > > > evaluated energy (COUL-SR) value of the polor atoms of the Arg and
> > > > > carboxylate as energygroup in my mdp file , and surprisingly I
> found
> > > > > the values are big positive numbers whereas I expected a negative
> > > > > values. Why the contradiction happens , trajectory showed
> attraction
> > > > > and energy is dispersion ?
> > > > >
> > > > > I just pasted few lines of the energy.xvg
> > > > > @ s0 legend "Coul-SR:Arg262_NH-CPG_COOH"
> > > > > @ s1 legend "Coul-14:Arg262_NH-CPG_COOH"
> > > > > 0.000000 5.647315 0.000000
> > > > > 2.000000 5.367461 0.000000
> > > > > 4.000000 6.109462 0.000000
> > > > > 6.000000 0.976809 0.000000
> > > > > 8.000000 4.306820 0.000000
> > > > > 10.000000 2.926659 0.000000
> > > > > 12.000000 2.567632 0.000000
> > > > > 14.000000 1.934579 0.000000
> > > > > 16.000000 3.874691 0.000000
> > > > > 18.000000 3.130555 0.000000
> > > > > 20.000000 1.804790 0.000000
> > > > >
> > > > > expecting you experts opinion on this.
> > > > >
> > > > > Regards,
> > > > > Raja
> > > > > --
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> > > >
> > > > --
> > > > _____________
> > > >
> > > > Prof. Dr. André Farias de Moura
> > > > Department of Chemistry
> > > > Federal University of São Carlos
> > > > São Carlos - Brazil
> > > > phone: +55-16-3351-8090
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> > _____________
> >
> > Prof. Dr. André Farias de Moura
> > Department of Chemistry
> > Federal University of São Carlos
> > São Carlos - Brazil
> > phone: +55-16-3351-8090
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