Re: [AMBER] Energy units in mm-pbsa calculations

From: <moitrayee.mbu.iisc.ernet.in>
Date: Fri, 26 Mar 2010 18:04:41 +0530 (IST)

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 - 06:30:04 PDT
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