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 ?
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
>> >> >>
>> >> >>
>> >> >> --
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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,
>> > University of Florida
>> > Ph.D. Graduate Student
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> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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