# Re: [AMBER] Problem with MMPBSA.py

From: Rajeswari A. <rajeswari.biotech.gmail.com>
Date: Wed, 9 Jul 2014 11:02:09 +0530

Hi Jason,

Thank you for your reply. As you mention, sander and MMPBSA_py_energy agree
well for the same input with same trajectory. When I did a run with
decomposition, mmpbsa used sander by default and gave me EPB of -41. Same
input without decomposition ran in MMPBSA_py_energy by default and gave me
EPB = -2109. I misunderstood that the difference might be due to the PBSA
solver. As per your suggestion i ran another set without decomposition and
used sander for solving PBSA. That agree well with the mmpbsa_py_energy.

Now i did not know why the run with additional decomposition analysis for
the same trajectory showed high degree of variation. For your reference I
am providing here the output files of two runs. Please suggest me what is
going wrong..

*Run1 with decomposition:*
Input file:
|--------------------------------------------------------------
| MMPBSA.py input file for running GB
| &general
| startframe=10001, endframe=10500, interval=5,
| keep_files=0, netcdf=1,
| /
| &pb
| istrng=0.15,
| /
| &decomp
| idecomp=4, dec_verbose=0, csv_format=0,
| /
|--------------------------------------------------------------
|MMPBSA.py Version=12.0
|Complex topology file: complex.top
|Receptor topology file: rec.top
|Ligand topology file: lig.top
|Initial mdcrd(s): striped.cdf
|
|
|Calculations performed using 100 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

POISSON BOLTZMANN:

Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1570.6463 18.5001
1.8500
EEL -14433.7714 67.0721
6.7072
EPB -41.7154 6.8142
0.6814
ENPOLAR 1608.3309 7.1545
0.7155
EDISPER -906.8760 6.2041
0.6204

G gas -16004.4177 65.6325
6.5633
G solv 659.7395 8.0241
0.8024

TOTAL -15344.6781 65.1341
6.5134

Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1444.2819 18.7405
1.8740
EEL -13784.9961 66.9163
6.6916
EPB -36.2793 8.3634
0.8363
ENPOLAR 1561.9777 7.1734
0.7173
EDISPER -920.1879 6.3128
0.6313

G gas -15229.2780 64.5246
6.4525
G solv 605.5105 9.1145
0.9115

TOTAL -14623.7675 62.4162
6.2416

Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -27.1840 2.0771
0.2077
EEL -582.6359 11.2582
1.1258
EPB -85.1861 4.5620
0.4562
ENPOLAR 116.3572 0.9017
0.0902
EDISPER -111.2425 0.7487
0.0749

G gas -609.8199 11.2676
1.1268
G solv -80.0714 4.5259
0.4526

TOTAL -689.8913 9.4012
0.9401

Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -99.1804 5.4152
0.5415
EEL -66.1394 16.2858
1.6286
EPB 79.7500 10.6530
1.0653
ENPOLAR -70.0040 2.0120
0.2012
EDISPER 124.5544 2.4387
0.2439

DELTA G gas -165.3198 15.9131
1.5913
DELTA G solv 134.3004 10.4657
1.0466

DELTA TOTAL -31.0193 16.1536
1.6154

*Run2 without decomposition:*
Input file:
|--------------------------------------------------------------
| MMPBSA.py input file for running GB
| &general
| startframe=10001, endframe=10500, interval=5,
| keep_files=0, netcdf=1, use_sander=1,
| /
| &pb
| istrng=0.15,
| /
|# &decomp
|# idecomp=4, dec_verbose=0, csv_format=0,
|# /
|--------------------------------------------------------------
|MMPBSA.py Version=12.0
|Complex topology file: 2pc_p2-nc_wt.top
|Receptor topology file: rec.top
|Ligand topology file: lig.top
|Initial mdcrd(s): striped.cdf
|
|
|Calculations performed using 100 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------

POISSON BOLTZMANN:

Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1570.6463 18.5001
1.8500
EEL -14433.7714 67.0721
6.7072
EPB -2109.0699 57.6319
5.7632
ENPOLAR 1608.3309 7.1545
0.7155
EDISPER -906.8760 6.2041
0.6204

G gas -16004.4177 65.6325
6.5633
G solv -1407.6150 57.6036
5.7604

TOTAL -17412.0327 32.8501
3.2850

Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -1444.2819 18.7405
1.8740
EEL -13784.9961 66.9163
6.6916
EPB -1977.9142 57.4849
5.7485
ENPOLAR 1561.9777 7.1734
0.7173
EDISPER -920.1879 6.3128
0.6313

G gas -15229.2780 64.5246
6.4525
G solv -1336.1244 57.3387
5.7339

TOTAL -16565.4024 31.1172
3.1117

Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -27.1840 2.0771
0.2077
EEL -582.6359 11.2582
1.1258
EPB -242.0701 6.4496
0.6450
ENPOLAR 116.3572 0.9017
0.0902
EDISPER -111.2425 0.7487
0.0749

G gas -609.8199 11.2676
1.1268
G solv -236.9553 6.4977
0.6498

TOTAL -846.7752 7.5375
0.7538

Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -99.1804 5.4152
0.5415
EEL -66.1394 16.2858
1.6286
EPB 110.9143 15.4282
1.5428
ENPOLAR -70.0040 2.0120
0.2012
EDISPER 124.5544 2.4387
0.2439

DELTA G gas -165.3198 15.9131
1.5913
DELTA G solv 165.4647 15.3900
1.5390

DELTA TOTAL 0.1450 6.9400
0.6940

On Tue, Jul 8, 2014 at 9:14 PM, Jason Swails <jason.swails.gmail.com> wrote:

> On Tue, Jul 8, 2014 at 7:07 AM, Rajeswari A. <rajeswari.biotech.gmail.com>
> wrote:
>
> > Dear Amber developers,
> >
> > I am running MMPBSA.py version 12 (AMBER12 + Ambertools12). However,
> when I
> > use PBSA solver in sander, the EPB term vary significantly with that of a
> > run that used mmpbsa_py_energy, for the same trajectory.
> >
> > For example EPB is -2109.0597 with mmpbsa_py_energy and -41.7154 with
> > sander.
> >
>
> ​This should not happen. sander and mmpbsa_py_energy (and pbsa) use the
> same PB code, and so should nominally give the same answer. There are some
> small setup changes between the two programs that I've noticed, so the
> energies don't match up exactly.
>
> However, when I run the test case with sander and compare with the values I
> get using mmpbsa_py_energy, the energies all agree to within 0.1 kcal/mol
> (0.01 kcal/mol for binding, which is well inside the uncertainty of the
> method itself).
>
> What is your input file? It could be that MMPBSA.py is not writing the
> input file for sander correctly. Although based on the sheer magnitude of
> your numbers, I would guess that you are comparing the receptor
> contribution calculated by mmpbsa_py_energy with the ligand contribution
> computed by sander (-2109 is the right order of magnitude for a large
> protein, while -40 is the right order of magnitude for a small ligand).
>
> ​​
> > Which one is better to use?
> >
>
> ​Run the Amber test suite. Do all of the tests pass?
>
> HTH,
> Jason
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

```--
Rajeswari A,
PhD Research Scholar,
Computational Biophysics Lab,
Department of Biotechnology,