With the parameters you have chosen in your input files (specifically
setting DCTYPE=4), the organization of your output file appears correct. The
first energy column was zero in the test case that we ran with the same
parameters, too. So that seems to be acceptable, although you should check
your statistics.out file to ensure that the numbers there seem reasonable as
well.
Good luck!
-Bill
On Thu, Mar 25, 2010 at 12:42 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> 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.plmodule
> >> 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 - 20:00:03 PDT
