AMBER Archive (2008)

Subject: Re: AMBER: MM-PBSA and delphi

From: Neha Gandhi (n.gandhiau_at_gmail.com)
Date: Mon Jun 09 2008 - 04:57:21 CDT

Thanks Navnit,

Thats what I realised after reading few more papers and references.

http://amber.scripps.edu/doc6/html/AMBER-sh-13.html

Revisiting free energy calculations: a theoretical connection to
MM/PBSA and direct calculation of the association free energy.
Biophys J. 2004 Jan;86(1 Pt 1):67-74

The above paper is excellent as it compares both the methods of single
and three state calculations.
Cheers,
Neha

On Mon, Jun 9, 2008 at 5:05 PM, Navnit Kumar Mishra
<navnit_at_chemi.muni.cz> wrote:
> Hello Neha;
>
> I am appending some informations regarding you query about interaction
> energy calculation.
>
> Neha Gandhi wrote:
>
>> Can I also use a single trajectory method in such case?
>>
>
> You can use single trajectory approach to compare the ligand affinity
> against one receptor, however, if you would like to include the ligand
> induced energy ( free energy of adaptation) which would be the difference in
> the free energy between the holo and apo state of the molecule, than you
> should use three separate trajectory approach.
> deltaG(adopt) = < Gmmpbsa(holo) > - < Gmmpbsa(apo) >
>
> The paper by Masukawa, et. al. /J. Med. Chem.,/ *46* (26), 5628 -5637, 2003.
> and /J. Am. Chem. Soc.,/ *128* (39), 12766 -12777, 2006. discused it in
> detail.
>
>> On Mon, Jun 9, 2008 at 1:49 PM, Neha Gandhi <n.gandhiau_at_gmail.com> wrote:
>>
>>>
>>> Dear Amber users,
>>>
>>> Can anybody tell me if I should use the final snapshots of the ligand,
>>> receptor and complex to run the final MM-PBSA script along with
>>> delphi? There is a conformational change in the complex.
>>>
>>>
>
> As you know the sampling issue is one of the key point for accurate binding
> energy calculation. So, the only one snapshot would not give you the overall
> averaged interaction energy, however, in vivo experiment overall
> conformational energy is measured. Thats why we use all the conformations
> which sampled during the dynamics, and then we averaged it to get <deltaE>.
> I would prefer to include all the conformations with a frequency of 10 or 20
> ps, I would leave the part of trajectory which is not fully equillibriated.
>
> with regards,
> Navnit
>
>>> --
>>> Regards,
>>> Neha Gandhi,
>>> School of Biomedical Sciences,
>>> Curtin University of Technology,
>>> GPO Box U1987 Perth,
>>> Western Australia 6845
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>>>
>>>
>>
>>
>>
>>
>
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-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
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