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
> >> >>
> >> >>
> >> >> --
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> >> >
> >> >
> >> >
> >> > --
> >> > Bill Miller III
> >> > Quantum Theory Project,
> >> > University of Florida
> >> > Ph.D. Graduate Student
> >> > 352-392-6715
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> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Aug 23 2010 - 05:00:07 PDT
