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 - 07:00:03 PDT
