You are right; there does appear to be something wrong here. :) It looks
like there is an inconsistency between the prmtops that you are giving
mm_pbsa.pl and the coordinate files that you extracted because of the *
extremely* high energy values that you are getting here. You should double
check that the coordinate files generated match with the prmtops you are
providing the program, possibly by visualizing them with your favorite
visualization program (VMD, Chimera, PyMOL, etc). Also, are there any error
messages or warnings in the logfile that could be useful?
On a side note, have you tried performing the MM-PBSA calculation with
MMPBSA.py? The process of generating snapshots is mostly transparent to the
user with this script and would be a way of determining if a prmtop/inpcrd
inconsistency is the problem here.
-Bill Miller
On Fri, Mar 26, 2010 at 8:34 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Thanks a lot for the reply.
>
> I encountered another problem with stability calculations.
> The output is as pasted below with huge values of PBTOT and GBTOT.
>
> # MEAN STD
> # =======================
> ELE 111173.29 866.98
> VDW 84569627.92 89181.67
> INT 89440034.73 26383643.99
> GAS 174120835.95 26383787.90
> PBSUR 0.00 0.00
> PBCAL -167771.24 2531.76
> PBSOL -167771.24 2531.76
> PBELE -56597.95 2537.82
> PBTOT 173953064.71 26383907.93
> GBSUR 0.00 0.00
> GB -171262.49 786.66
> GBSOL -171262.49 786.66
> GBELE -60089.20 517.04
> GBTOT 173949573.45 26383648.93
>
> This looks unreasonable.
>
> The input file is attached. Please suggest me on this problem.
> Thanks a lot once again.
>
> Best Regards,
> Moitrayee
>
>
>
>
> > 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 Fri Mar 26 2010 - 07:00:02 PDT
