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
Received on Mon Aug 23 2010 - 04:30:05 PDT
