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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> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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Received on Mon Aug 23 2010 - 05:00:05 PDT
