You could always run MM-PBSA on only one frame to get the pair-wise
interaction energies for a single structure.
You could also use a sander input for pairwise decomposition (idecomp=2 or
4) and set imin=5 (for post-processing analysis). Then just run the sander
command using the '-y' flag to indicate the single-frame
trajectory/coordinate file that you want to analyze.
Good luck!
-Bill
On Sat, Mar 27, 2010 at 2:59 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
> Thanks a lot. There was inconsistency between my prmtops and coordinates.
> Now i
> am getting meaningful values
>
> Is there a way to obtain pairwise interaction energies between residues (
> as we
> get from mm-pbsa using DCTYPE=4) without running a simulation but from a
> single
> structure in AMBER ?
>
> Any help regarding this matter will be greatly appreciated.
> Thanks once again.
>
> Best Regards,
> Moitrayee
>
>
> > 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 Sat Mar 27 2010 - 07:30:03 PDT
