Hi Jason,
Thanks a lot for your reply.
I have a small doubt. The solvation terms are Gpolar (esurf) and Gnes (sas).
They, I presume are free energy terms. On the other hand eel, vdw and internal
energies are interaction energies.
Gtot = Gsolute + Gsolvent
= Usolute - Tdelta(S) + Gpolar + Gnes
where Usolute = Eint+Eeel+Evdw, S is the entropy term. Gtot is the free energy
of interaction between any two given residues.
As you suggested the total value for each residue in my calculation is =>
Eint + Eeel + Evdw + esurf + sas
It is devoid of the entropy term. So what do I call this term. Is it the energy
of interaction between two given residues in solution ? I am going to do an
elaborate calculation starting with this energy values and so want to be sure of
the basics. I would be grateful if you please clarify.
I would eagerly look forward to hear from you.
Thanks once again.
Regards,
Moitrayee
> 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
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>> >> >> >>
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Bill Miller III
>> >> >> > Quantum Theory Project,
>> >> >> > University of Florida
>> >> >> > Ph.D. Graduate Student
>> >> >> > 352-392-6715
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>> >> > Quantum Theory Project,
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>> >> > Ph.D. Graduate Student
>> >> > 352-392-6715
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>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Graduate Student
>> > 352-392-6715
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>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Tue Aug 24 2010 - 02:30:03 PDT
