HI,
My former memory was allocated 3000 mb, so this time I tried 5000 and 8000 respectively. I ever remembered, I ever successful calculated the entropy for only one ligand and one subunit only. But for two subunits, it never work. It may be this problem.
Thanks,
Rilei Yu
--- 10年6月5日，周六, Dwight McGee <dwight.mcgee.gmail.com> 写道：
发件人: Dwight McGee <dwight.mcgee.gmail.com>
主题: Re: [AMBER] entropy calculation failed again!
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年6月5日,周六,上午11:02
Since your convergence was satisfied it appears to be a memory problem. The
entropy calculation can used more than 2GB of memory so I would suggest
trying to run this on a machine with more memory.
On Fri, Jun 4, 2010 at 10:44 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Here is the information I can obtain:
> ----Convergence Satisfied----
>
> allocation failure in vector: nh = 440496144
>
> Rilei Yu
>
> --- 10年6月5日，周六, Bill Miller III <brmilleriii.gmail.com> 写道：
>
> 发件人: Bill Miller III <brmilleriii.gmail.com>
> 主题: Re: [AMBER] entropy calculation failed again!
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2010年6月5日,周六,上午9:35
>
> 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
>
>
>
>
> _______________________________________________
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> 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 - 22:00:04 PDT
