I'm not able to reproduce the results given in this link
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htmwhen
using Amber19 Pmemd (CUDA) to run the simulations. Particularly my EEL/EPB
values are significantly different even though my delta Gtotal values are
similar to what is expected. I have changed the input files quite a few
times to try and get a closer result but regardless i'm getting deviated
values in both the PB and GB electrostatics. Is this to be expected? Below
is my mmpbsa output file for PB only as this is where he EEL/EPB deviations
are more apparent.
Â
| Run on Wed Jul  3 11:47:48 2019
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| Â startframe=300,endframe=500,interval=10,keep_files=2,
|/
|&pb
| Â istrng=0.100, inp=1, radiopt=0, fillratio=4.0, cavity_surften=0.0072,
cavity_offset=0.86
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: Â SOLV.prmtop
|Complex topology file: Â Â Â Â Â complex-ante.prmtop
|Receptor topology file: Â Â Â Â Â receptor-ante.prmtop
|Ligand topology file: Â Â Â Â Â Â ligand-ante.prmtop
|Initial mdcrd(s): Â Â Â Â Â Â Â
 ../Production_Simulation/MD_1.mdcrd
|
|Receptor mask: Â Â Â Â Â Â Â Â Â ":1-242"
|Ligand mask: Â Â Â Â Â Â Â Â Â Â ":243"
|Ligand residue name is "LIG"
|
|Calculations performed using 21 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|All units are reported in kcal/mole.
----------------------------------------------------------------------------
---
----------------------------------------------------------------------------
---
Â
POISSON BOLTZMANN:
Â
Complex:
Energy Component       Average        Std. Dev. Â
Std. Err. of Mean
----------------------------------------------------------------------------
---
VDWAALS Â Â Â Â Â Â Â Â Â -2008.9413 Â Â Â Â Â Â Â 21.5994 Â
      4.7134
EEL Â Â Â Â Â Â Â Â Â Â -16893.8777 Â Â Â Â Â Â Â 54.0189
      11.7879
EPB Â Â Â Â Â Â Â Â Â Â Â -2939.6031 Â Â Â Â Â Â Â 42.5845
       9.2927
ENPOLAR Â Â Â Â Â Â Â Â Â Â 93.6548 Â Â Â Â Â Â Â Â 1.1848
       0.2585
Â
G gas          -18902.8190        49.1428 Â
     10.7238
G solv          -2845.9484        42.6445 Â
      9.3058
Â
TOTAL Â Â Â Â Â Â Â Â Â -21748.7674 Â Â Â Â Â Â Â 55.0018 Â
     12.0024
Â
Receptor:
Energy Component       Average        Std. Dev. Â
Std. Err. of Mean
----------------------------------------------------------------------------
---
VDWAALS Â Â Â Â Â Â Â Â Â -1947.4382 Â Â Â Â Â Â Â 21.0682 Â
      4.5975
EEL Â Â Â Â Â Â Â Â Â Â -16750.5690 Â Â Â Â Â Â Â 57.9642
      12.6488
EPB Â Â Â Â Â Â Â Â Â Â Â -3079.3301 Â Â Â Â Â Â Â 51.3910
      11.2144
ENPOLAR Â Â Â Â Â Â Â Â Â Â 95.9442 Â Â Â Â Â Â Â Â 1.1311
       0.2468
Â
G gas          -18698.0072        51.5286 Â
     11.2445
G solv          -2983.3859        51.7566 Â
     11.2942
Â
TOTAL Â Â Â Â Â Â Â Â Â -21681.3930 Â Â Â Â Â Â Â 51.1759 Â
     11.1675
Â
Ligand:
Energy Component       Average        Std. Dev. Â
Std. Err. of Mean
----------------------------------------------------------------------------
---
VDWAALS Â Â Â Â Â Â Â Â Â Â -4.7575 Â Â Â Â Â Â Â Â 1.3592
       0.2966
EEL Â Â Â Â Â Â Â Â Â Â Â Â 48.2262 Â Â Â Â Â Â Â
 3.3345        0.7276
EPB Â Â Â Â Â Â Â Â Â Â Â Â -79.0733 Â Â Â Â Â Â Â
 1.1124        0.2428
ENPOLAR Â Â Â Â Â Â Â Â Â Â Â 6.5719 Â Â Â Â Â Â Â Â 0.0418
       0.0091
Â
G gas            43.4687         3.6361
       0.7935
G solv           -72.5014         1.1072
       0.2416
Â
TOTAL Â Â Â Â Â Â Â Â Â Â Â -29.0327 Â Â Â Â Â Â Â Â 2.8527
       0.6225
Â
Differences (Complex - Receptor - Ligand):
Energy Component       Average        Std. Dev. Â
Std. Err. of Mean
----------------------------------------------------------------------------
---
VDWAALS Â Â Â Â Â Â Â Â Â Â -56.7456 Â Â Â Â Â Â Â Â 2.7554
       0.6013
EEL Â Â Â Â Â Â Â Â Â Â Â -191.5350 Â Â Â Â Â Â Â 23.9159
       5.2189
EPB Â Â Â Â Â Â Â Â Â Â Â Â 218.8003 Â Â Â Â Â Â Â 19.7621
       4.3124
ENPOLAR Â Â Â Â Â Â Â Â Â Â -8.8614 Â Â Â Â Â Â Â Â 0.3138
       0.0685
EDISPER Â Â Â Â Â Â Â Â Â Â Â 0.0000 Â Â Â Â Â Â Â Â 0.0000
       0.0000
Â
DELTA G gas        -248.2805        25.2482 Â
      5.5096
DELTA G solv        209.9389        19.8835 Â
      4.3389
Â
DELTA TOTAL Â Â Â Â Â Â Â Â -38.3416 Â Â Â Â Â Â Â Â 7.2458 Â
      1.5812
Â
----------------------------------------------------------------------------
---
----------------------------------------------------------------------------
---
Â
Thanking you in advance,
Â
Aswin Hanagal
Â
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Received on Wed Jul 10 2019 - 08:30:02 PDT
