I have not tested against AmberTools 12 yet but I've also got a dG which
seems too high. I have however checked with mm_pbsa.pl and the results
are totally different: DELTA TOTAL = -9.6205 vs PBTOT = -47.07.
The protocols are not fully compatible I suppose but I add the relevant
output below.
| Run on Thu Jun 27 23:49:39 2013
|
|Input file:
|--------------------------------------------------------------
|test
|&general
| startframe = 1, endframe = 999999, interval = 1,
| entropy = 0,
| keep_files = 0, debug_printlevel = 2
|/
|&pb
| istrng = 0.0, scale = 2.0, fillratio = 4.0,
| indi = 1.0, exdi = 80.0,
| radiopt = 0,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: solvated.parm7
|Complex topology file: com.parm7
|Receptor topology file: rec.parm7
|Ligand topology file: lig.parm7
|Initial mdcrd(s): ../../md009.nc
|
|Receptor mask: ":1-280"
|Ligand mask: ":281"
|Ligand residue name is "LIG"
|
|Calculations performed using 50 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2305.7377 24.4924 3.4637
EEL -19919.1740 89.2244 12.6182
EPB -3534.0664 58.9115 8.3313
ENPOLAR 2285.5894 8.7376 1.2357
EDISPER -1276.2335 9.3054 1.3160
G gas -22224.9117 85.0597 12.0293
G solv -2524.7105 57.4060 8.1184
TOTAL -24749.6222 48.2806 6.8279
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2241.5015 24.3427 3.4426
EEL -19929.6399 88.5651 12.5250
EPB -3552.5783 58.7668 8.3109
ENPOLAR 2272.3010 8.6985 1.2302
EDISPER -1293.3993 9.1478 1.2937
G gas -22171.1415 84.9844 12.0186
G solv -2573.6767 57.0945 8.0744
TOTAL -24744.8181 48.7507 6.8944
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -4.6870 1.4285 0.2020
EEL 40.5490 3.5986 0.5089
EPB -31.6343 2.0657 0.2921
ENPOLAR 53.2980 0.3144 0.0445
EDISPER -52.7092 0.4826 0.0682
G gas 35.8620 3.4403 0.4865
G solv -31.0455 1.9698 0.2786
TOTAL 4.8165 2.8743 0.4065
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -59.5492 2.3688 0.3350
EEL -30.0831 5.7671 0.8156
EPB 50.1463 4.3827 0.6198
ENPOLAR -40.0096 1.0869 0.1537
EDISPER 69.8750 1.3036 0.1844
DELTA G gas -89.6322 6.2040 0.8774
DELTA G solv 80.0117 4.7020 0.6650
DELTA TOTAL -9.6205 4.1658 0.5891
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
==============================================================================
=>> Reading input parameters
Found PREFIX => snapshot
Found PATH => ./
Found COMPLEX => 1
Found RECEPTOR => 1
Found LIGAND => 1
Found COMPT => ./com.parm7
Found RECPT => ./rec.parm7
Found LIGPT => ./lig.parm7
Found GC => 0
Found AS => 0
Found DC => 0
Found MM => 1
Found GB => 1
Found PB => 1
Found MS => 1
Found NM => 0
Found PROC => 2
Found REFE => 0
Found INDI => 1.0
Found EXDI => 80.0
Found SCALE => 2
Found LINIT => 1000
Found PRBRAD => 1.4
Found ISTRNG => 0.0
Found RADIOPT => 0
Found NPOPT => 1
Found CAVITY_SURFTEN => 0.0072
Found CAVITY_OFFSET => 0.00
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found DIELC => 1.0
Found IGB => 2
Found GBSA => 1
Found SALTCON => 0.00
Found EXTDIEL => 80.0
Found INTDIEL => 1.0
Found SURFTEN => 0.0072
Found SURFOFF => 0.00
Found PROBE => 0.0
[...]
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7801.06 83.87 -7555.04 83.97 -215.94 2.82
VDW -1245.53 30.99 -1203.22 30.83 17.24 2.22
INT 8227.47 49.91 8158.65 48.76 68.83 5.34
GAS -819.12 82.77 -599.61 83.08 -129.87 5.76
PBSUR 103.67 0.86 105.56 0.86 5.76 0.07
PBCAL -3534.03 59.66 -3552.59 59.50 -31.66 2.07
PBSOL -3430.36 59.61 -3447.03 59.42 -25.90 2.07
PBELE -11335.09 37.87 -11107.63 37.76 -247.59 1.68
PBTOT -4249.48 51.61 -4046.64 50.41 -155.77 4.94
GBSUR 103.67 0.86 105.56 0.86 5.76 0.07
GB -3670.19 67.35 -3686.32 67.43 -28.32 2.18
GBSOL -3566.52 67.28 -3580.76 67.34 -22.56 2.18
GBELE -11471.25 33.06 -11241.36 32.53 -244.25 1.42
GBTOT -4385.64 50.50 -4180.37 48.82 -152.43 4.86
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -30.08 5.83
VDW -59.55 2.39
INT 0.00 0.00
GAS -89.63 6.27
PBSUR -7.65 0.18
PBCAL 50.22 4.44
PBSOL 42.57 4.40
PBELE 20.13 3.79
PBTOT -47.07 3.83
GBSUR -7.65 0.18
GB 44.45 4.00
GBSOL 36.80 3.96
GBELE 14.36 3.19
GBTOT -52.84 3.16
Cheers,
Hannes.
On Thu, 27 Jun 2013 12:44:21 -0400
Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jun 27, 2013 at 12:02 PM, <psu4.uic.edu> wrote:
>
> > Dear Amber 12,
> >
> > We found that the mmPBSA calculation results are quite
> > different from MMPBSA.py in AmberTools 12 & AmberTools 13. The
> > MMPBSA.py AmberTools 12 results (dG) seem to be very negative just
> > like AmberTools 1.5 (dG= -30~-40 kcal/mol) while MMPBSA.py
> > AmberTools 13 results are less negative. (dG= -7 ~ -9 kcal/mol).
>
>
> >
> > We find that the default setting of "radiopt" has been changed
> > from 1 (AmberTools 12) to 0 (AmberTools 13). However, even set
> > radiop = 1 in AmberTools 13 and use the same other settings and
> > parameter files (radi) to run mmPBSA, MMPBSA.py results in
> > AmberTools 13 are still less negative than AmberTools12. *May we
> > know if there is a major change of the MMPBSA.py algorithm in
> > AmberTools 13? *
> >
> >
>
> MMPBSA.py itself has not changed how it works. It continues to call
> external programs to compute the energies of each snapshot. If the
> binding free energy results change between two versions of MMPBSA.py,
> that's a result of changes to whichever programs that it calls.
>
> The PB code changes a lot more than the GB code (the latter should
> never change), so differences in results between two versions are
> unfortunately not unusual. In my experience the differences have
> never been that large, though.
>
> However, where is the bulk of the difference in the binding free
> energy coming from? Is the electrostatic energy largely the same?
> Is most of the difference coming from big changes to the non-polar
> solvation free energy? Looking at the actual energy terms that change
> significantly will help narrow down what might have changed from one
> version to the next. Not being an active PBSA developer, though, I'm
> not sure what has changed between AmberTools 13 and AmberTools 12.
>
> HTH,
> Jason
>
--
Scanned by iCritical.
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Received on Fri Jun 28 2013 - 01:30:03 PDT
