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
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Received on Fri Jun 04 2010 - 20:00:03 PDT
