Thanks a lot for your reply.
Is there a way by which I can consider all interactions between two residues
except the backbone-backbone component? (i.e sidechain of first and sidechain
and backbone of second + backbone of first and the sidechain of second)
Thanks a lot in advance for any help.
Sincere Regards,
Moitrayee
> The SGBTOT represents the interaction of the sidechain of the first residue
with both the sidechain and backbone of the second residue. BGBTOT represents
the interaction of the backbone of the first residue with both the sidechain and
backbone of the second residue. TGBTOT represents the entire first residue
interaction with the entire second residue.
>
> Hope this helps,
> Jason
>
> On Wed, Apr 7, 2010 at 8:42 AM, <moitrayee.mbu.iisc.ernet.in> wrote:
>> 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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> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Wed Apr 07 2010 - 22:30:03 PDT
