Hello,
The decomposition separates the energy contributions from internal (Bond,
angle, dihedral, and 1-4 interactions depending on what idecomp model you
chose), eel, vdw, and solvation terms (esurf/sas). You can just look at the
total value for each residue to take into account the solvation effects as
well.
On Mon, Aug 23, 2010 at 7:47 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Is there a way I can calculate the ones in solution.
> As you suggested
>
> "Do you mean getting the interaction energy between two solvent-exposed
> >> amino
> >> > acid residues? You should be able to do this by simply defining the
> print
> >> > residue option in your mm_pbsa.pl input file (COMPRI, RECPRI, and
> >> LIGPRI) to
> >> > print only those two residues."
>
> or atleast get an an approximation using any module of AMBER ?
> What do the GB and SAS mean physically ?
>
GB basically takes into account the free energy required to polarize the
solvent in response to the solute charge distribution. It's an average over
all degrees of freedom of the solvent molecules, which is why it eliminates
a lot of the noise typically associated with explicit solvent calculations.
This is the "electrostatic" contribution to the solvation free energy.
There is also a non-electrostatic portion, included in GBSA, such as that
due to the hydrophobic effect, which is taken to be proportional to the
solvent accessible surface area. The amber manual has a decent introduction
to GB and can point you to more detailed articles for information.
Good luck!
Jason
> Thanks a lot.
>
> Sincere Regards,
> Moitrayee
>
> > The interaction energies Einternal, Eele, and Evdw correspond to the
> > interaction energies in vacuum.
> >
> > -Bill
> >
> > On Mon, Aug 23, 2010 at 7:35 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> >
> >> The decomp.in file is attached with this email.
> >> Sorry for the mistake.
> >>
> >> Sincere Regards,
> >> Moitrayee
> >>
> >>
> >> ------------------------------- Original Message
> >> -------------------------------
> >> Subject: Re: [AMBER] Interaction energy_mm_pbsa
> >> From: moitrayee.mbu.iisc.ernet.in
> >> Date: Mon, August 23, 2010 5:03 pm
> >> To: "AMBER Mailing List" <amber.ambermd.org>
> >>
> >>
> --------------------------------------------------------------------------------
> >>
> >> Thanks a lot for your reply.
> >>
> >> I am attaching the decomp.in file i have used for the calculation. I
> have
> >> indeed
> >> defined the print residue option in the attached decomp.in file
> (COMPRI,
> >> RECPRI,
> >> and LIGPRI) to print all the interaction energies between the desired
> >> residues
> >> (558 such residues). Now I get an output for each snapshot, the first
> few
> >> lines
> >> are pasted below.
> >>
> >> MM
> >> GB
> >> MS
> >> 1
> >> TDC 1-> 1 0.000 3.041 -16.427 -68.876 667.066
> >> TDC 1-> 2 0.000 -0.220 -7.064 -1.980 -140.104
> >> TDC 1-> 3 0.000 -0.238 -3.355 2.931 -7.882
> >> TDC 1-> 4 0.000 -0.870 -0.285 -0.102 -138.963
> >> TDC 1-> 5 0.000 -0.020 -0.192 0.171 0.000
> >> TDC 1-> 6 0.000 -0.002 -0.254 0.249 0.000
> >>
> >>
> >> I understand that the 4th column is internal energy, 5th is vdw, 6th
> ele,
> >> 7th GB
> >> and 8th gamma*SAS.
> >>
> >> Now are the interaction energy values (i.e Einternal+Eele+Evdw) reflect
> the
> >> realistic interaction energies in solvent or are they representing
> >> interaction
> >> energies if the two residues were in vacuum?
> >>
> >> I would look forward to hear from you.
> >> Thanks once again.
> >>
> >> Sincere Regards,
> >> Moitrayee
> >>
> >> > Do you mean getting the interaction energy between two solvent-exposed
> >> amino
> >> > acid residues? You should be able to do this by simply defining the
> print
> >> > residue option in your mm_pbsa.pl input file (COMPRI, RECPRI, and
> >> LIGPRI) to
> >> > print only those two residues.
> >> >
> >> > -Bill
> >> >
> >> > On Mon, Aug 23, 2010 at 7:15 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> >> >
> >> >> Thanks a lot for your email.
> >> >>
> >> >> I am using mm-pbsa for obtaining the pairwise interaction energies
> >> between
> >> >> the
> >> >> different amino acid residues in the complex.
> >> >>
> >> >> Can you please suggest me how I can realistically obtain the
> interaction
> >> >> energies (ele+vdw) of a residue pair in solvent.
> >> >>
> >> >> Thanks once again.
> >> >>
> >> >> Sincere Regards,
> >> >> Moitrayee
> >> >>
> >> >> > Direct interaction energies between the solvent and solute would be
> >> >> > difficult to calculate using MM-PBSA. You would have to treat the
> >> water
> >> >> > molecules as part of the complex, and this complicates several
> aspects
> >> of
> >> >> > the calculation itself. Plus, you would also probably need to
> include
> >> >> > solvent-solvent interactions in the calculation, too, and this
> would
> >> >> > overwhelm the energetics of the system, making the actual binding
> >> energy
> >> >> > difficult to discern. MM-PBSA is primarily used as a way to
> >> approximate
> >> >> the
> >> >> > binding energy without explicitly taking account the solvent in the
> >> >> energy
> >> >> > calculation.
> >> >> >
> >> >> > I hope this helps.
> >> >> >
> >> >> > -Bill
> >> >> >
> >> >> >
> >> >> > On Mon, Aug 23, 2010 at 6:17 AM, <moitrayee.mbu.iisc.ernet.in>
> wrote:
> >> >> >
> >> >> >> Dear Amber Users,
> >> >> >>
> >> >> >> I am trying to obtain pairwise interaction energies between amino
> >> acid
> >> >> >> residues
> >> >> >> from mm_pbsa. The interaction energies obtained (Eele+Evdw+Eint)
> are
> >> the
> >> >> >> gas
> >> >> >> phase energies as suggested in the tutorial. However, a more
> >> realistic
> >> >> >> value
> >> >> >> would be the interaction energy taking into consideration the
> solvent
> >> >> >> effect.
> >> >> >>
> >> >> >> So Eint = Egas+Esolvent
> >> >> >>
> >> >> >> = Eij + Ei-solv + Ej-solv
> >> >> >>
> >> >> >> where i, j are two residues and solv is the solvent.
> >> >> >>
> >> >> >> >From the parameters obtained from the decomposed pairwise
> >> interaction
> >> >> >> energies,
> >> >> >> is it possible to derive the above.
> >> >> >> Or is it that I am going wrong somewhere in the basic
> understanding.
> >> >> >>
> >> >> >> I would be grateful if someone please clarifies my confusion.
> >> >> >> Thanks a lot in advance.
> >> >> >>
> >> >> >> Sincere Regards,
> >> >> >> Moitrayee
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> This message has been scanned for viruses and
> >> >> >> dangerous content by MailScanner, and is
> >> >> >> believed to be clean.
> >> >> >>
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Bill Miller III
> >> >> > Quantum Theory Project,
> >> >> > University of Florida
> >> >> > Ph.D. Graduate Student
> >> >> > 352-392-6715
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >> > --
> >> >> > This message has been scanned for viruses and
> >> >> > dangerous content by MailScanner, and is
> >> >> > believed to be clean.
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> This message has been scanned for viruses and
> >> >> dangerous content by MailScanner, and is
> >> >> believed to be clean.
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Bill Miller III
> >> > Quantum Theory Project,
> >> > University of Florida
> >> > Ph.D. Graduate Student
> >> > 352-392-6715
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> > --
> >> > This message has been scanned for viruses and
> >> > dangerous content by MailScanner, and is
> >> > believed to be clean.
> >> >
> >> >
> >>
> >>
> >> --
> >> This message has been scanned for viruses and
> >> dangerous content by MailScanner, and is
> >> believed to be clean.
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > This message has been scanned for viruses and
> > dangerous content by MailScanner, and is
> > believed to be clean.
> >
> >
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 23 2010 - 06:30:04 PDT
