Hi Tan,
>>TOTAL term or the sum of Electrostatic term and Polar Solvation?
It iis better to take the pair than to look at them individually, yes
the right calculation to run depends on how you want to relate your
simulation to reality, and what is the type of 'effect' that you are
interested in. If you want to know the structural or functional effects of
charged residues, compare two MD simulations, one of which has the charged
residues mutated to alanine. Use cpptraj to count hydrogen bonds, or
pymol to make nice graphics, and you are done. This is a great simulation
to do because it can be compared to experiment. Another
empirically-relatable simulation is to turn up the amount of salt, thus
reducing the range of electrostatic interactions.
If you want to analyse thermodynamics and write down a number for some kind
of energy contribution per-residue then this is philosophically difficult
as protein-solvent interaction is not just the sum of the individual amino
acids. This type of calculation makes the most sense when you have a
well-defined reference: when you find the free energy gain to make a salt
bridge, for instance, you have to have an idea whether you are comparing
against the same structure in an unfolded conformation without the salt
bridge, or against a mutant with a non-polar sidechain, or against the same
salt bridge but with electrostatics somehow deleted. The last is easiest,
you just use parmed to set the charge of the appropriate sidechains to
zero, but this is also the least physical.
Dr Josh Berryman
Uni Luxembourg
On Wed, 10 Jul 2019 at 13:06, 谭畅 <tanc.sioc.ac.cn> wrote:
>
> Thanks for your replication. So the most useful term of decomposition
> MMGBSA is TOTAL term or the sum of Electrostatic term and Polar Solvation?
> Actually I want to know the effect of Charged residues on interaction
> between my complex. If there are any better methods please tell me.
> Best wishes!
>
> > -----原始邮件-----
> > 发件人: "Josh Berryman" <the.real.josh.berryman.gmail.com>
> > 发送时间: 2019-07-10 17:38:04 (星期三)
> > 收件人: "AMBER Mailing List" <amber.ambermd.org>
> > 抄送:
> > 主题: Re: [AMBER] electrostatic energy of mmgbsa decomposition
> >
> > Hi Tan, in a GB calculation there is some interaction between the
> solvation
> > part of the energy and the direct (Coulomb) terms, the full equation is
> > complicated and the decomposition into two terms in the output file isn't
> > very useful. If you add up the GBSA and EELEC terms then the combined
> > total ought to behave more like you expect (ie it should be more negative
> > when a salt bridge is formed, etc).
> >
> > Dr Josh Berryman
> > Uni Luxembourg
> >
> >
> >
> > On Wed, 10 Jul 2019 at 09:50, 谭畅 <tanc.sioc.ac.cn> wrote:
> >
> > > Hi everyone! I just calculate the mmgbsa decomposition of my complex.
> And
> > > I got the output file including electrostatic energy. But I found
> there are
> > > something strange. For example,I found the electrostatic value of a
> Glu is
> > > positive. But when I view the interaction of the complex around this
> Glu I
> > > found no negative residue around it. Oppositely, there are several
> positive
> > > residues around it. Shouldn`t it be more stable and its value be more
> > > negative? Would you tell me the fundamental of the decomposition
> mmgbsa and
> > > electrostatic energy?
> > >
> > > Best wishes!
> > > _______________________________________________
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> > >
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Received on Thu Jul 11 2019 - 05:00:02 PDT
