[gmx-users] Coul-SR: positive value for interating group

Raj D gromacs.for.f at gmail.com
Thu May 28 07:08:27 CEST 2015


Thanks Dr Mark your points are well taken.
Regards,
Raja
On May 28, 2015 1:46 AM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

> 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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