Dear Bill Miller,
Thanks a lot for your reply.
I am perfprming a residue wise decomposition using mm-pbsa. I have pasted below
a segment of my results.
Residue No. INT ELE VDW GB SASA
TDC 1-> 1 0.000 1.481 -10.800 -62.602 955.437
TDC 1-> 2 0.000 -0.719 -10.437 -0.766 -147.459
TDC 1-> 3 0.000 -0.384 -0.807 0.486 -73.536
I have the following questions
1. Are the energy units for each term kcal/mol here also ?
2. All INTs for all my residue pairs are zero; is that alright ?
3. SASA is not energy; E(SAS) = gamma(SASA)+beta
what are the values for gamma and beta ?
Thanks a lot in advance for any help.
Best Regards,
Moitrayee
> The energy units of GBTOT and PBTOT are in kcal/mol. Your analysis of your
> results seem valid. You get different free energies of binding during
> different parts of the simulation because the complex is simply not in the
> exact same conformation during all of those different time intervals. I
> think a more appropriate free energy of binding calculation would include a
> long simulation time in order for the calculation to include as many
> relevant conformations of the complex as possible. This should give a free
> energy of binding that is more agreeable with the true dynamics of the
> system.
>
> I hope that helps.
>
> -Bill Miller
>
> On Tue, Mar 23, 2010 at 8:57 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
>
>> Dear Amber Users,
>>
>> I am doing a stability calculation of a protein using mm-pbsa.pl module of
>> AMBER9. What are the units of GBTOT and PBTOT. Is it kcal/mol ?
>> Also I have performed the calculations over snapshots collected from
>> different
>> time intervals of the trajectory e.g. 5-7ns, 10-13 ns and 15-17 ns. I get
>> different values for GBTOT and PBTOT for each set. However, GBTOT and PBTOT
>> within a set are highly convergent. Can this effect arise due to small
>> conformation changes within a simulation.
>> Looking forward to hear from you.
>> Thanks a lot in advance for any help.
>>
>> Sincere Regards,
>> Moitrayee Bhattacharyya
>> Molecular Biophysics Unit
>> Indian institute of Science
>> Bangalore - 560012
>> India
>>
>>
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Received on Thu Mar 25 2010 - 04:30:03 PDT
