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 - 01:00:03 PDT
