This looks like a memory allocation error. Because this is a relatively
large system (432 residues), you will need quite a bit of RAM to perform
this calculation. On the test system for the tutorial, a 267 residue system
required >2 GB of RAM for the calculation of the complex alone. How much
memory are you allocating for this calculation? You might want to try giving
it more memory for the calculation.
Also, what output file did you get this error from? There should have been
three nmode output files (_MMPBSA_complex_nm.out, _MMPBSA_receptor_nm.out,
and _MMPBSA_ligand_nm.out). Did all of these files give this error? Or was
it just one or two of the files? Logically, the ligand nmode calculation
should have been performed without errors because there should be plenty of
memory available to do the nmode calculation on only a two residue ligand.
-Bill
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
>
>
>
>
> _______________________________________________
> 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
Received on Fri Jun 04 2010 - 20:30:03 PDT
