Re: [AMBER] Energy units in mm-pbsa calculations

From: <moitrayee.mbu.iisc.ernet.in>
Date: Thu, 25 Mar 2010 22:12:10 +0530 (IST)

The input file and output are attached. The output file has been attached for 4
snapshots.
Thanks a lot for your help.

Best Regards,
Moitrayee

> The energy units here are all kcal/mol, also. I'm not really sure what is
> going on with all your internal energies being zero. Could you attach your
> input and an output file, such as com.all.out? This might give is a better
> understanding of what's going on. The gamma and beta from the SASA
> calculation are surften and surfoff, respectively, in your input file. The
> example mm_pbsa.pl input in the AMBER manual sets these values at 0.0072 and
> 0.00, respectively. However, these values can be changed by the user if
> desired
>
> -Bill
>
> On Thu, Mar 25, 2010 at 6:44 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
>
>> 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 - 10:30:04 PDT
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