I forgot to attach the output file I got here it is for A 3.2
Thanks again,
Fabian
| Run on Mon Oct 19 17:02:08 2015
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| endframe=50, keep_files=2,
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&pb
| istrng=0.100,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: 1err.solvated.prmtop
|Complex topology file: complex.prmtop
|Receptor topology file: receptor.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): 1err_prod.mdcrd
|
|Receptor mask: ":1-240"
|Ligand mask: ":241"
|Ligand residue name is "RAL"
|
|Calculations performed using 50 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in mmpbsa_py_energy
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2013.3861 20.1108 2.8441
EEL -16938.6434 84.8707 12.0025
EGB -3506.9860 67.1003 9.4894
ESURF 97.4744 1.3170 0.1863
G gas -18952.0295 81.3542 11.5052
G solv -3409.5116 66.5951 9.4180
TOTAL -22361.5411 36.3100 5.1350
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1955.2346 19.0529 2.6945
EEL -16895.0333 84.6812 11.9757
EGB -3528.7058 67.6664 9.5695
ESURF 101.2621 1.2926 0.1828
G gas -18850.2679 80.7202 11.4156
G solv -3427.4437 67.2065 9.5044
TOTAL -22277.7116 34.9512 4.9428
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1.8595 2.0320 0.2874
EEL -5.5800 2.0133 0.2847
EGB -28.4852 0.5979 0.0846
ESURF 4.4805 0.0425 0.0060
G gas -7.4395 3.0299 0.4285
G solv -24.0047 0.6040 0.0854
TOTAL -31.4442 3.2513 0.4598
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956 0.4095
EEL -38.0301 3.1822 0.4500
EGB 50.2050 2.5622 0.3624
ESURF -8.2682 0.2700 0.0382
DELTA G gas -94.3222 3.3476 0.4734
DELTA G solv 41.9369 2.4569 0.3475
DELTA TOTAL -52.3853 2.4400 0.3451
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2013.3861 20.1108 2.8441
EEL -16938.6434 84.8707 12.0025
EPB -3243.9257 65.3247 9.2383
ENPOLAR 1965.5188 6.3800 0.9023
EDISPER -1107.5209 6.8746 0.9722
G gas -18952.0295 81.3542 11.5052
G solv -2385.9278 64.1430 9.0712
TOTAL -21337.9573 41.6819 5.8947
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1955.2346 19.0529 2.6945
EEL -16895.0333 84.6812 11.9757
EPB -3269.9142 65.8450 9.3119
ENPOLAR 1956.8205 6.3089 0.8922
EDISPER -1131.1692 6.4443 0.9114
G gas -18850.2679 80.7202 11.4156
G solv -2444.2629 64.7289 9.1540
TOTAL -21294.5308 40.4319 5.7179
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1.8595 2.0320 0.2874
EEL -5.5800 2.0133 0.2847
EPB -30.7649 0.6756 0.0955
ENPOLAR 52.1180 0.2043 0.0289
EDISPER -50.6514 0.3305 0.0467
G gas -7.4395 3.0299 0.4285
G solv -29.2984 0.7439 0.1052
TOTAL -36.7378 3.0716 0.4344
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956 0.4095
EEL -38.0301 3.1822 0.4500
EPB 56.7534 3.5086 0.4962
ENPOLAR -43.4196 1.2202 0.1726
EDISPER 74.2997 1.3514 0.1911
DELTA G gas -94.3222 3.3476 0.4734
DELTA G solv 87.6335 3.8311 0.5418
DELTA TOTAL -6.6887 3.8564 0.5454
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
____________________
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
> On 19 Oct 2015, at 5:17 PM, Fabian gmail <fabian.glaser.gmail.com> wrote:
>
> Dear Amber colleagues,
>
> I am doing all the MMPBSA tutorials, and I found consistently that while the GENERALISED BORN results are almost identical to the tutorial (using the tutorial .mdrcd and .prmtop files) the POISSON BOLTZMANN results are completely different. As I said I only did the MMPBSA.py calculation, using given files. For example using the following command for tutorial files A 3.2 (http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm <http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm>) I got the following FINAL_RESULTS_MMPBSA.dat file, which as you see for the POISSON BOLTZMANN yields a much lower DELTA TOTAL -6.6887 compared to the tutorial DELTA G binding = -41.7256 !!
>
> Why is that?????
>
> As explained above the GENERALISED BORN results are much more similar, for my calculation is DELTA TOTAL -52.3853 and the tutorial is DELTA G binding = -52.2672. That is great.
>
> I used the command and input files provided on the tutorial:
>
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp 1err.solvated.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y *.mdcrd
>
> I want to test this method on several systems, so it’s important for me to understand the differences…. any hint will really help me. The same happens on 3.1 so I suspect there is something different or wrong with the calculation.
>
> Thanks a lot in advance,
>
> Fabian
>
> ____________________
> Dr. Fabian Glaser
>
> Head of the Structural Bioinformatics section
>
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
>
> fglaser at technion dot ac dot il
> Tel: +972 4 8293701
> http://bku.technion.ac.il <http://bku.technion.ac.il/>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 19 2015 - 07:30:04 PDT
