Thanks Ray,
Can you advise how or what to set the surface tension coefficients at?
My understanding is that if inp=2, then I need to use:
radiopt=1, cavity_surften=0.005, cavity_offset= 0.86
however, when I add those to the input I get the following error.
Beginning PB calculations with /home/jonathan/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /home/jonathan/amber12/bin/mmpbsa_py_energy failed with prmtop
../complex.prmtop!
Exiting. All files have been retained
Where _MMPBSA_complex_pb.mdout.0
only has the following:
Reading parm file (../complex.prmtop)
title:
default_name
mm_options: e_debug=3
mm_options: ipb=2
mm_options: inp=2
mm_options: epsin=1.000000
mm_options: epsout=80.000000
mm_options: smoothopt=1
mm_options: istrng=100.000000
mm_options: radiopt=1
mm_options: dprob=1.400000
mm_options: iprob=2.000000
mm_options: npbopt=0
mm_options: solvopt=1
mm_options: accept=0.001000
mm_options: maxitn=1000
mm_options: fillratio=4.000000
mm_options: space=0.500000
mm_options: nfocus=2
mm_options: fscale=8
mm_options: bcopt=5
mm_options: eneopt=2
mm_options: cutnb=0.000000
mm_options: sprob=0.557000
mm_options: cavity_surften=0.005000
mm_options: cavity_offset=0.860000
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar EPB
frms
eff.c(2660) enb14 --> 349.324
eff.c(2661) eel14 --> 3470.015
I got a similar error previously when I left out the default paramaters -
inp=1, radiopt=0
On Thu, Dec 20, 2012 at 2:05 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> You are not setting the surface tension coefficients for the nonpolar
> solvation energy. The default values were for inp=2. If you look at
> the EPB and EGB, they are qualitatively consistent.
>
> Ray
>
> On Thu, Dec 20, 2012 at 10:58 AM, Jonathan Gough
> <jonathan.d.gough.gmail.com> wrote:
> > Tried again with basic generic parameters. The PB results are
> > still bizarre.
> >
> > I'm getting the same values on 2 different machines using 2 different
> OS's
> >
> > Files are attached.
> >
> > | Run on Thu Dec 20 13:46:36 2012
> > |
> > |Input file:
> > |--------------------------------------------------------------
> > |Input file for running PB and GB
> > |&general
> > | interval=10,
> > | verbose=1,
> > |# entropy=1,
> > |/
> > |&gb
> > | saltcon=0.100
> > |/
> > |&pb
> > | istrng=0.100, inp=1, radiopt=0
> > |/
> > |&alanine_scanning
> > |/
> > |--------------------------------------------------------------
> > |MMPBSA.py Version=12.0
> > |Solvated complex topology file: ../eq9-tip3.prmtop
> > |Complex topology file: ../complex.prmtop
> > |Receptor topology file: ../protein.prmtop
> > |Ligand topology file: ../peptide.prmtop
> > |Mutant complex topology file: complex103.prmtop
> > |Mutant receptor topology file: ../protein.prmtop
> > |Mutant ligand topology file: peptide103.prmtop
> > |Initial mdcrd(s): prod1.mdcrd.gz
> > |
> > |Receptor mask: ":1-87"
> > |Ligand mask: ":88-106"
> > |
> > |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.
> >
> -------------------------------------------------------------------------------
> >
> -------------------------------------------------------------------------------
> >
> > GENERALIZED BORN:
> >
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -682.0769 18.1879
> > 2.5722
> > EEL -7105.7544 89.2399
> > 12.6204
> > EGB -1761.1677 86.3443
> > 12.2109
> > ESURF 53.3449 2.1585
> > 0.3053
> >
> > G gas -7787.8313 96.7750
> > 13.6861
> > G solv -1707.8227 84.8790
> > 12.0037
> >
> > TOTAL -9495.6540 29.2096
> > 4.1309
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -533.1672 13.2827
> > 1.8785
> > EEL -5893.7948 63.9261
> > 9.0405
> > EGB -1484.4252 64.3861
> > 9.1056
> > ESURF 47.8004 1.2265
> > 0.1734
> >
> > G gas -6426.9620 65.9628
> > 9.3285
> > G solv -1436.6247 63.5284
> > 8.9843
> >
> > TOTAL -7863.5867 21.2503
> > 3.0052
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -51.4980 4.9814
> > 0.7045
> > EEL -1112.7783 32.3386
> > 4.5734
> > EGB -431.0815 28.6901
> > 4.0574
> > ESURF 17.2915 0.2743
> > 0.0388
> >
> > G gas -1164.2764 31.9185
> > 4.5140
> > G solv -413.7901 28.5145
> > 4.0326
> >
> > TOTAL -1578.0664 10.4672
> > 1.4803
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -97.4117 14.5839
> > 2.0625
> > EEL -99.1813 28.4013
> > 4.0166
> > EGB 154.3390 31.8477
> > 4.5039
> > ESURF -11.7470 1.7622
> > 0.2492
> >
> > DELTA G gas -196.5929 38.2549
> > 5.4101
> > DELTA G solv 142.5921 30.4919
> > 4.3122
> >
> > DELTA TOTAL -54.0009 9.8976
> > 1.3997
> >
> >
> >
> -------------------------------------------------------------------------------
> >
> -------------------------------------------------------------------------------
> > K103A MUTANT:
> > GENERALIZED BORN:
> >
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -676.7151 17.8731
> > 2.5276
> > EEL -6952.8738 78.5670
> > 11.1111
> > EGB -1849.4765 75.0327
> > 10.6112
> > ESURF 53.7723 2.0673
> > 0.2924
> >
> > G gas -7629.5889 83.9892
> > 11.8779
> > G solv -1795.7042 73.8494
> > 10.4439
> >
> > TOTAL -9425.2932 28.2685
> > 3.9978
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -533.1672 13.2827
> > 1.8785
> > EEL -5893.7948 63.9261
> > 9.0405
> > EGB -1484.4252 64.3861
> > 9.1056
> > ESURF 47.8004 1.2265
> > 0.1734
> >
> > G gas -6426.9620 65.9628
> > 9.3285
> > G solv -1436.6247 63.5284
> > 8.9843
> >
> > TOTAL -7863.5867 21.2503
> > 3.0052
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -50.2227 4.8232
> > 0.6821
> > EEL -1016.8797 17.7425
> > 2.5092
> > EGB -457.0862 14.1321
> > 1.9986
> > ESURF 17.2581 0.2073
> > 0.0293
> >
> > G gas -1067.1023 17.7434
> > 2.5093
> > G solv -439.8281 14.0642
> > 1.9890
> >
> > TOTAL -1506.9304 10.0612
> > 1.4229
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -93.3253 14.0196
> > 1.9827
> > EEL -42.1993 27.3134
> > 3.8627
> > EGB 92.0348 27.6026
> > 3.9036
> > ESURF -11.2862 1.7042
> > 0.2410
> >
> > DELTA G gas -135.5246 33.3161
> > 4.7116
> > DELTA G solv 80.7486 26.7078
> > 3.7771
> >
> > DELTA TOTAL -54.7760 9.4931
> > 1.3425
> >
> >
> >
> -------------------------------------------------------------------------------
> >
> -------------------------------------------------------------------------------
> >
> > RESULT OF ALANINE SCANNING: (K103A) DELTA DELTA G binding = 0.7751
> +/-
> > 1.6145
> >
> -------------------------------------------------------------------------------
> >
> -------------------------------------------------------------------------------
> >
> > POISSON BOLTZMANN:
> >
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -682.0769 18.1879
> > 2.5722
> > EEL -7105.7544 89.2399
> > 12.6204
> > EPB -1843.3860 84.3276
> > 11.9257
> > ENPOLAR -7895.3567 338.1798
> > 47.8258
> >
> > G gas -7787.8313 96.7750
> > 13.6861
> > G solv -9738.7428 394.3993
> > 55.7765
> >
> > TOTAL -17526.5741 327.0635
> > 46.2538
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -533.1672 13.2827
> > 1.8785
> > EEL -5893.7948 63.9261
> > 9.0405
> > EPB -1542.5632 63.4845
> > 8.9781
> > ENPOLAR -7113.1093 149.7471
> > 21.1774
> >
> > G gas -6426.9620 65.9628
> > 9.3285
> > G solv -8655.6724 200.2324
> > 28.3171
> >
> > TOTAL -15082.6345 155.0666
> > 21.9297
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -51.4980 4.9814
> > 0.7045
> > EEL -1112.7783 32.3386
> > 4.5734
> > EPB -441.3410 28.3329
> > 4.0069
> > ENPOLAR -2792.9997 46.4237
> > 6.5653
> >
> > G gas -1164.2764 31.9185
> > 4.5140
> > G solv -3234.3407 63.5687
> > 8.9900
> >
> > TOTAL -4398.6171 45.0261
> > 6.3677
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -97.4117 14.5839
> > 2.0625
> > EEL -99.1813 28.4013
> > 4.0166
> > EPB 140.5181 31.4729
> > 4.4509
> > ENPOLAR 2010.7523 295.3602
> > 41.7702
> > EDISPER 0.0000 0.0000
> > 0.0000
> >
> > DELTA G gas -196.5929 38.2549
> > 5.4101
> > DELTA G solv 2151.2704 317.7442
> > 44.9358
> >
> > DELTA TOTAL 1954.6774 287.7796
> > 40.6982
> >
> >
> >
> -------------------------------------------------------------------------------
> >
> -------------------------------------------------------------------------------
> > K103A MUTANT:
> > POISSON BOLTZMANN:
> >
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -676.7151 17.8731
> > 2.5276
> > EEL -6952.8738 78.5670
> > 11.1111
> > EPB -1926.0225 73.7476
> > 10.4295
> > ENPOLAR -7897.2824 325.3416
> > 46.0103
> >
> > G gas -7629.5889 83.9892
> > 11.8779
> > G solv -9823.3049 366.5358
> > 51.8360
> >
> > TOTAL -17452.8938 315.8032
> > 44.6613
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -533.1672 13.2827
> > 1.8785
> > EEL -5893.7948 63.9261
> > 9.0405
> > EPB -1542.5632 63.4845
> > 8.9781
> > ENPOLAR -7113.1093 149.7471
> > 21.1774
> >
> > G gas -6426.9620 65.9628
> > 9.3285
> > G solv -8655.6724 200.2324
> > 28.3171
> >
> > TOTAL -15082.6345 155.0666
> > 21.9297
> >
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -50.2227 4.8232
> > 0.6821
> > EEL -1016.8797 17.7425
> > 2.5092
> > EPB -463.7980 13.1878
> > 1.8650
> > ENPOLAR -2704.9421 40.8040
> > 5.7706
> >
> > G gas -1067.1023 17.7434
> > 2.5093
> > G solv -3168.7402 46.8262
> > 6.6222
> >
> > TOTAL -4235.8425 40.0329
> > 5.6615
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> >
> -------------------------------------------------------------------------------
> > VDWAALS -93.3253 14.0196
> > 1.9827
> > EEL -42.1993 27.3134
> > 3.8627
> > EPB 80.3387 27.9239
> > 3.9490
> > ENPOLAR 1920.7690 283.2766
> > 40.0614
> > EDISPER 0.0000 0.0000
> > 0.0000
> >
> > DELTA G gas -135.5246 33.3161
> > 4.7116
> > DELTA G solv 2001.1077 296.5305
> > 41.9357
> >
> > DELTA TOTAL 1865.5831 275.8093
> > 39.0053
> >
> >
> >
> -------------------------------------------------------------------------------
> >
> -------------------------------------------------------------------------------
> >
> > RESULT OF ALANINE SCANNING: (K103A) DELTA DELTA G binding = 89.0943
> +/-
> > 22.5695
> >
> -------------------------------------------------------------------------------
> >
> -------------------------------------------------------------------------------
> >
> >
> >
> > On Wed, Dec 19, 2012 at 11:20 AM, Jonathan Gough <
> jonathan.d.gough.gmail.com
> >> wrote:
> >
> >> I ran a MMPBSA computation and the data isn't exactly what I expected.
> I
> >> am wondering if and what I am missing. Do these results make sense?
> >>
> >> protein - peptide MD was done in explicit solvent, 1 Na atom was used
> for
> >> charge balance.
> >>
> >> the total G is negative for the GB, but the PB is positive.
> >>
> >>
> >> |Input file:
> >> |--------------------------------------------------------------
> >> |Input file for running PB and GB
> >> |&general
> >> | interval=10,
> >> | verbose=1,
> >> |# entropy=1,
> >> |/
> >> |&gb
> >> | igb=2, saltcon=0.10
> >> |/
> >> |&pb
> >> | istrng=0.000, inp=1, radiopt=0
> >> |/
> >> |--------------------------------------------------------------
> >> |MMPBSA.py Version=12.0
> >> |Solvated complex topology file: eq9-tip3.prmtop
> >> |Complex topology file: complex.prmtop
> >> |Receptor topology file: protein.prmtop
> >> |Ligand topology file: peptide.prmtop
> >> |Initial mdcrd(s): prod10.mdcrd.gz
> >> | prod1.mdcrd.gz
> >> | prod2.mdcrd.gz
> >> | prod3.mdcrd.gz
> >> | prod4.mdcrd.gz
> >> | prod5.mdcrd.gz
> >> | prod6.mdcrd.gz
> >> | prod7.mdcrd.gz
> >> | prod8.mdcrd.gz
> >> | prod9.mdcrd.gz
> >> |
> >> |Receptor mask: ":1-87"
> >> |Ligand mask: ":88-106"
> >> |
> >> |Calculations performed using 500 complex frames.
> >> |Poisson Boltzmann calculations performed using internal PBSA solver in
> >> mmpbsa_py_energy
> >> |
> >> |All units are reported in kcal/mole.
> >>
> >>
> -------------------------------------------------------------------------------
> >>
> >>
> -------------------------------------------------------------------------------
> >>
> >> GENERALIZED BORN:
> >>
> >> Complex:
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -689.3528 20.3887
> >> 0.9118
> >> EEL -7209.9961 101.0713
> >> 4.5200
> >> EGB -1780.7197 95.8827
> >> 4.2880
> >> ESURF 51.4798 2.2001
> >> 0.0984
> >>
> >> G gas -7899.3488 106.4936
> >> 4.7625
> >> G solv -1729.2399 94.4497
> >> 4.2239
> >>
> >> TOTAL -9628.5887 32.2263
> >> 1.4412
> >>
> >>
> >> Receptor:
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -538.6278 13.0420
> >> 0.5833
> >> EEL -5947.4782 77.6774
> >> 3.4738
> >> EGB -1529.2047 67.3836
> >> 3.0135
> >> ESURF 46.7337 1.1744
> >> 0.0525
> >>
> >> G gas -6486.1060 79.4018
> >> 3.5510
> >> G solv -1482.4710 66.6187
> >> 2.9793
> >>
> >> TOTAL -7968.5770 29.5391
> >> 1.3210
> >>
> >>
> >> Ligand:
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -53.1702 4.4720
> >> 0.2000
> >> EEL -1071.2554 35.6834
> >> 1.5958
> >> EGB -484.7833 29.3741
> >> 1.3136
> >> ESURF 17.6407 0.3696
> >> 0.0165
> >>
> >> G gas -1124.4256 35.4379
> >> 1.5848
> >> G solv -467.1426 29.1083
> >> 1.3018
> >>
> >> TOTAL -1591.5682 12.9770
> >> 0.5803
> >>
> >>
> >> Differences (Complex - Receptor - Ligand):
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -97.5548 14.2769
> >> 0.6385
> >> EEL -191.2625 72.3842
> >> 3.2371
> >> EGB 233.2682 69.9734
> >> 3.1293
> >> ESURF -12.8945 1.9697
> >> 0.0881
> >>
> >> DELTA G gas -288.8172 79.1380
> >> 3.5392
> >> DELTA G solv 220.3737 68.5420
> >> 3.0653
> >>
> >> DELTA TOTAL -68.4435 13.1973
> >> 0.5902
> >>
> >>
> >>
> >>
> -------------------------------------------------------------------------------
> >>
> >>
> -------------------------------------------------------------------------------
> >>
> >> POISSON BOLTZMANN:
> >>
> >> Complex:
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -689.3528 20.3887
> >> 0.9118
> >> EEL -7209.9961 101.0713
> >> 4.5200
> >> EPB -1733.3105 92.7881
> >> 4.1496
> >> ENPOLAR -7646.4575 330.6507
> >> 14.7871
> >>
> >> G gas -7899.3488 106.4936
> >> 4.7625
> >> G solv -9379.7680 389.7384
> >> 17.4296
> >>
> >> TOTAL -17279.1168 324.8458
> >> 14.5275
> >>
> >>
> >> Receptor:
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -538.6278 13.0420
> >> 0.5833
> >> EEL -5947.4782 77.6774
> >> 3.4738
> >> EPB -1490.9879 65.4619
> >> 2.9275
> >> ENPOLAR -6960.8637 146.4187
> >> 6.5480
> >>
> >> G gas -6486.1060 79.4018
> >> 3.5510
> >> G solv -8451.8517 192.4196
> >> 8.6053
> >>
> >> TOTAL -14937.9577 141.5962
> >> 6.3324
> >>
> >>
> >> Ligand:
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -53.1702 4.4720
> >> 0.2000
> >> EEL -1071.2554 35.6834
> >> 1.5958
> >> EPB -470.2825 28.6124
> >> 1.2796
> >> ENPOLAR -2836.5168 53.5764
> >> 2.3960
> >>
> >> G gas -1124.4256 35.4379
> >> 1.5848
> >> G solv -3306.7993 74.0624
> >> 3.3122
> >>
> >> TOTAL -4431.2249 49.5550
> >> 2.2162
> >>
> >>
> >> Differences (Complex - Receptor - Ligand):
> >> Energy Component Average Std. Dev. Std. Err.
> of
> >> Mean
> >>
> >>
> -------------------------------------------------------------------------------
> >> VDWAALS -97.5548 14.2769
> >> 0.6385
> >> EEL -191.2625 72.3842
> >> 3.2371
> >> EPB 227.9599 68.7656
> >> 3.0753
> >> ENPOLAR 2150.9231 302.5804
> >> 13.5318
> >> EDISPER 0.0000 0.0000
> >> 0.0000
> >>
> >> DELTA G gas -288.8172 79.1380
> >> 3.5392
> >> DELTA G solv 2378.8830 351.2831
> >> 15.7099
> >>
> >> DELTA TOTAL 2090.0658 293.9258
> >> 13.1448
> >>
> >>
> >>
> >>
> -------------------------------------------------------------------------------
> >>
> >>
> -------------------------------------------------------------------------------
> >>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Thu Dec 20 2012 - 12:00:02 PST
