When I do pairwise decomposition of interaction energies in mm-pbsa, there are 3
components: SGBTOT (side-chain), BGBTOT(backbone), and TGBTOT(total). Which of
the component has the sidechain-backbone interaction terms.
Any help regarding this matter will be greatly appreciated.
Many thanks and Regards,
Moitrayee
> 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 Wed Apr 07 2010 - 06:30:02 PDT
