Hi,
Seeing that you have a fairly large system of 420 residues you may want to
increase your convergence criterion or increase the number or cycles. The
message printed in your output is printed if your system fails to meet the
convergence criterion after two attempts.
On Fri, Jun 4, 2010 at 9:35 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> The FINAL_RESULTS_MMPBSA.dat file will probably not have the useful
> information that you are looking for. Have you looked in the logfile from
> the calculation? Also, the nmode output files would be a great place to
> look
> for some helpful information. Take a look in the _MMPBSA_complex_nm.out,
> _MMPBSA_receptor_nm.out, and _MMPBSA_ligand_nm.out files and see if there
> is
> some error or warning messages in those files?
>
> I hope this sheds some light on the issue.
>
> -Bill
>
> On Fri, Jun 4, 2010 at 9:28 PM, Rilei Yu <yulaomao1983.yahoo.com.cn>
> wrote:
>
> >
> > After waiting for three days, the entropy calculation for one frame of my
> > system was finished! Unfortunately, all results showed to me is NO NMODE
> > ENTROPY CALCULATED. SNAPSHOTS NOT MINIMIZED!
> >
> > It looks like my system is so special that entropy calculation cannot be
> > performed. Is this time still the converge problem using updated script?
> To
> > this point, I am a bit of disappointed!
> >
> > The results as follows:
> > | Run on Sat Jun 5 04:42:48 EST 2010
> >
> > |Input file:
> > |--------------------------------------------------------------
> > |MMPBSA everything
> > |&general
> > | startframe=1, endframe=1,
> > | entropy=0, keep_files=0,
> > |/
> > |&gb
> > | igb=5, saltcon=0.15,
> > |/
> > |&pb
> > | istrng=0.15,
> > |# sander_apbs=1,
> > |/
> > |&nmode
> > | maxcyc=50000, ala_entropy=0, nmode_istrng=0.15,
> > |/
> > |
> > |
> > |
> > |
> > |--------------------------------------------------------------
> > |Complex topology file: complex.prmtop
> > |Receptor topology file: re.prmtop
> > |Ligand topology file: lig.prmtop
> > |Initial mdcrd(s): complex_md0.mdcrd
> > |
> > |Best guess for receptor mask: ":1-420"
> > |Best guess for ligand mask: ":421-432"
> >
> > |Calculations performed using 1 frames.
> > |NMODE calculations performed using 1 frames.
> > |Poisson Boltzmann calculations performed using internal PBSA solver in
> > sander.
> > |
> > |All units are reported in kcal/mole.
> > |All entropy results have units kcal/mole (Temperature is 298.15 K).
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> > NO NMODE ENTROPY CALCULATED. SNAPSHOTS NOT MINIMIZED!
> >
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> >
> > GENERALIZED BORN:
> >
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -3836.8981 0.0000
> > 0.0000
> > EEL -29831.2025 0.0000
> > 0.0000
> > EGB -4275.4807 0.0000
> > 0.0000
> > ESURF 142.3725 0.0000
> > 0.0000
> >
> > G gas -33668.1006 0.0000
> > 0.0000
> > G solv -4133.1082 0.0000
> > 0.0000
> >
> > TOTAL -37801.2088 0.0000
> > 0.0000
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -3702.0048 0.0000
> > 0.0000
> > EEL -28994.9903 0.0000
> > 0.0000
> > EGB -4145.3888 0.0000
> > 0.0000
> > ESURF 144.4286 0.0000
> > 0.0000
> >
> > G gas -32696.9951 0.0000
> > 0.0000
> > G solv -4000.9602 0.0000
> > 0.0000
> >
> > TOTAL -36697.9553 0.0000
> > 0.0000
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -48.8611 0.0000
> > 0.0000
> > EEL -783.3506 0.0000
> > 0.0000
> > EGB -217.3343 0.0000
> > 0.0000
> > ESURF 9.1300 0.0000
> > 0.0000
> >
> > G gas -832.2117 0.0000
> > 0.0000
> > G solv -208.2043 0.0000
> > 0.0000
> >
> > TOTAL -1040.4160 0.0000
> > 0.0000
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -86.0322 0.0000
> > 0.0000
> > EEL -52.8616 0.0000
> > 0.0000
> > EGB 87.2424 0.0000
> > 0.0000
> > ESURF -11.1861 0.0000
> > 0.0000
> >
> > DELTA G gas -138.8938 0.0000
> > 0.0000
> > DELTA G solv 76.0563 0.0000
> > 0.0000
> >
> >
> > DELTA G binding = -62.8375 +/- 0.0000
> > 0.0000
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> > Using Normal Mode Entropy Approximation: DELTA G binding = -62.8375
> > +/- 0.0000
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> >
> > POISSON BOLTZMANN:
> >
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -3836.8981 0.0000
> > 0.0000
> > EEL -29831.2025 0.0000
> > 0.0000
> > EPB -4242.3267 0.0000
> > 0.0000
> > ECAVITY 106.2150 0.0000
> > 0.0000
> >
> > G gas -33668.1006 0.0000
> > 0.0000
> > G solv -4136.1117 0.0000
> > 0.0000
> >
> > TOTAL -37804.2123 0.0000
> > 0.0000
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -3702.0048 0.0000
> > 0.0000
> > EEL -28994.9903 0.0000
> > 0.0000
> > EPB -4112.4700 0.0000
> > 0.0000
> > ECAVITY 107.7342 0.0000
> > 0.0000
> >
> > G gas -32696.9951 0.0000
> > 0.0000
> > G solv -4004.7358 0.0000
> > 0.0000
> >
> > TOTAL -36701.7309 0.0000
> > 0.0000
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -48.8611 0.0000
> > 0.0000
> > EEL -783.3506 0.0000
> > 0.0000
> > EPB -220.4057 0.0000
> > 0.0000
> > ECAVITY 5.8770 0.0000
> > 0.0000
> >
> > G gas -832.2117 0.0000
> > 0.0000
> > G solv -214.5287 0.0000
> > 0.0000
> >
> > TOTAL -1046.7404 0.0000
> > 0.0000
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> >
> -------------------------------------------------------------------------------
> > VDWAALS -86.0322 0.0000
> > 0.0000
> > EEL -52.8616 0.0000
> > 0.0000
> > EPB 90.5490 0.0000
> > 0.0000
> > ECAVITY -7.3962 0.0000
> > 0.0000
> >
> > DELTA G gas -138.8938 0.0000
> > 0.0000
> > DELTA G solv 83.1528 0.0000
> > 0.0000
> >
> >
> >
> > DELTA G binding = -55.7410 +/- 0.0000
> > 0.0000
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> > Using Normal Mode Entropy Approximation: DELTA G binding = -55.7410
> > +/- 0.0000
> >
> >
> -------------------------------------------------------------------------------
> >
> >
> -------------------------------------------------------------------------------
> >
> > I have to admit that it works well for little system.BUt it is not the
> same
> > story for my system. Here, I am sorry for my complain.
> >
> > Best wishes,
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Fri Jun 04 2010 - 19:30:03 PDT
