Hi,
inp=2 is default.
you are using default radii set for pb, therefore I would recommend you to rerun your pb and gb calculations with mbondi2 or mbondi3 (you can modify your prmtop file using parmed)
just add these keywords to your &pb section
inp=2, radiopt=0,
For PB, you may also change the internal dielectric constant.
indi=(1,2 or 4) try 2 and 4 and check the results. the current results are with indi=1 (default).
PB is sensitive to all these variables
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: NADIA RAHMAH [nadiiarah.apps.ipb.ac.id]
Sent: 07 July 2017 08:08
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA Delta total results
I am using AMBER16
On Fri, Jul 7, 2017 at 9:03 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Dear Ray,
> Just a correction.
> inp=2 is default in amber14 and amber17
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Ray Luo [rluo.uci.edu]
> Sent: 07 July 2017 01:04
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA Delta total results
>
> That's because you used inp=2 for pb. If you use inp=1, your pb and gb
> energies will be more similar.
>
> Looks like you are using the amber 14 release. The default has been
> set to inp=1 in newer releases.
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical Physics, Biomedical Engineering, and Chemical Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
>
> On Thu, Jul 6, 2017 at 2:49 AM, NADIA RAHMAH <nadiiarah.apps.ipb.ac.id>
> wrote:
> > Sorry to send not complete results. I didnt tell you this is PB Delta G.
> PB
> > Delta total value is positive while GB Delta is negaive, Is it problem or
> > something error?
> >
> > |Input file:
> > |--------------------------------------------------------------
> > |Sample input file for GB and PB calculation
> > |&general
> > |startframe=1, endframe=10000, interval=50,
> > |verbose=2, keep_files=0,
> > |/
> > |&gb
> > |igb=5, saltcon=0.150,
> > |/
> > |&pb
> > |istrng=0.15, fillratio=4.0
> > |/
> > |--------------------------------------------------------------
> > |MMPBSA.py Version=14.0
> > |Complex topology file: complexnobox_3wi7rbb.prmtop
> > |Receptor topology file: protein.prmtop
> > |Ligand topology file: ligan.prmtop
> > |Initial mdcrd(s): 3wi7rbb.nc
> > |
> > |Receptor mask: ":1-291"
> > |Ligand mask: ":292"
> > |Ligand residue name is "UNL"
> > |
> > |Calculations performed using 200 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
> > ------------------------------------------------------------
> -------------------
> > BOND 912.5936 23.3491
> > 1.6510
> > ANGLE 2428.7787 34.2154
> > 2.4194
> > DIHED 3769.6586 21.4600
> > 1.5175
> > VDWAALS -2466.7203 22.2716
> > 1.5748
> > EEL -19829.1418 106.3164
> > 7.5177
> > 1-4 VDW 1084.1896 14.5553
> > 1.0292
> > 1-4 EEL 9856.0973 41.1595
> > 2.9104
> > EGB -2557.6201 85.2699
> > 6.0295
> > ESURF 89.0527 1.7420
> > 0.1232
> >
> > G gas -4244.5444 103.4226
> > 7.3131
> > G solv -2468.5674 84.5367
> > 5.9776
> >
> > TOTAL -6713.1118 51.4808
> > 3.6402
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> -------------------
> > BOND 911.3783 23.2978
> > 1.6474
> > ANGLE 2422.5641 34.0504
> > 2.4077
> > DIHED 3768.2360 21.4450
> > 1.5164
> > VDWAALS -2448.4510 22.0682
> > 1.5605
> > EEL -19821.6598 106.3786
> > 7.5221
> > 1-4 VDW 1083.3272 14.6062
> > 1.0328
> > 1-4 EEL 9857.1039 41.1947
> > 2.9129
> > EGB -2565.1932 85.3334
> > 6.0340
> > ESURF 89.9441 1.7262
> > 0.1221
> >
> > G gas -4227.5013 104.0079
> > 7.3545
> > G solv -2475.2491 84.5944
> > 5.9817
> >
> > TOTAL -6702.7503 51.5860
> > 3.6477
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> -------------------
> > BOND 1.2152 0.9774
> > 0.0691
> > ANGLE 6.2146 2.0044
> > 0.1417
> > DIHED 1.4225 0.6671
> > 0.0472
> > VDWAALS -0.0078 0.3911
> > 0.0277
> > EEL -0.4298 0.2128
> > 0.0150
> > 1-4 VDW 0.8625 0.4192
> > 0.0296
> > 1-4 EEL -1.0066 0.2333
> > 0.0165
> > EGB -2.4506 0.0873
> > 0.0062
> > ESURF 1.6260 0.0096
> > 0.0007
> >
> > G gas 8.2706 2.4641
> > 0.1742
> > G solv -0.8245 0.0865
> > 0.0061
> >
> > TOTAL 7.4461 2.4730
> > 0.1749
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> -------------------
> > BOND -0.0000 0.0001
> > 0.0000
> > ANGLE 0.0000 0.0001
> > 0.0000
> > DIHED 0.0000 0.0000
> > 0.0000
> > VDWAALS -18.2614 1.2729
> > 0.0900
> > EEL -7.0523 1.8874
> > 0.1335
> > 1-4 VDW -0.0000 0.0001
> > 0.0000
> > 1-4 EEL -0.0000 0.0000
> > 0.0000
> > EGB 10.0237 1.5415
> > 0.1090
> > ESURF -2.5175 0.0801
> > 0.0057
> >
> > DELTA G gas -25.3137 2.2277
> > 0.1575
> > DELTA G solv 7.5062 1.5431
> > 0.1091
> >
> > DELTA TOTAL -17.8075 1.8112
> > 0.1281
> >
> >
> > ------------------------------------------------------------
> -------------------
> > ------------------------------------------------------------
> -------------------
> >
> > POISSON BOLTZMANN:
> >
> > Complex:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> -------------------
> > BOND 912.5936 23.3491
> > 1.6510
> > ANGLE 2428.7787 34.2154
> > 2.4194
> > DIHED 3769.6586 21.4600
> > 1.5175
> > VDWAALS -2466.7203 22.2716
> > 1.5748
> > EEL -19829.1418 106.3164
> > 7.5177
> > 1-4 VDW 1084.1896 14.5553
> > 1.0292
> > 1-4 EEL 9856.0973 41.1595
> > 2.9104
> > EPB -2639.8863 86.9608
> > 6.1491
> > ENPOLAR 2191.4591 8.4002
> > 0.5940
> > EDISPER -1130.7876 9.7908
> > 0.6923
> >
> > G gas -4244.5444 103.4226
> > 7.3131
> > G solv -1579.2148 86.0073
> > 6.0816
> >
> > TOTAL -5823.7592 56.4697
> > 3.9930
> >
> >
> > Receptor:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> -------------------
> > BOND 911.3783 23.2978
> > 1.6474
> > ANGLE 2422.5641 34.0504
> > 2.4077
> > DIHED 3768.2360 21.4450
> > 1.5164
> > VDWAALS -2448.4510 22.0682
> > 1.5605
> > EEL -19821.6598 106.3786
> > 7.5221
> > 1-4 VDW 1083.3272 14.6062
> > 1.0328
> > 1-4 EEL 9857.1039 41.1947
> > 2.9129
> > EPB -2660.8632 86.9206
> > 6.1462
> > ENPOLAR 2190.4601 8.3759
> > 0.5923
> > EDISPER -1139.5953 9.7842
> > 0.6919
> >
> > G gas -4227.5013 104.0079
> > 7.3545
> > G solv -1609.9985 85.9000
> > 6.0740
> >
> > TOTAL -5837.4998 55.4874
> > 3.9235
> >
> > Ligand:
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> -------------------
> > BOND 1.2152 0.9774
> > 0.0691
> > ANGLE 6.2146 2.0044
> > 0.1417
> > DIHED 1.4225 0.6671
> > 0.0472
> > VDWAALS -0.0078 0.3911
> > 0.0277
> > EEL -0.4298 0.2128
> > 0.0150
> > 1-4 VDW 0.8625 0.4192
> > 0.0296
> > 1-4 EEL -1.0066 0.2333
> > 0.0165
> > EPB -2.2980 0.0776
> > 0.0055
> > ENPOLAR 14.9804 0.1359
> > 0.0096
> > EDISPER -13.3213 0.0859
> > 0.0061
> >
> > G gas 8.2706 2.4641
> > 0.1742
> > G solv -0.6389 0.1582
> > 0.0112
> >
> > TOTAL 7.6317 2.4782
> > 0.1752
> >
> >
> > Differences (Complex - Receptor - Ligand):
> > Energy Component Average Std. Dev. Std. Err. of
> > Mean
> > ------------------------------------------------------------
> -------------------
> > BOND -0.0000 0.0001
> > 0.0000
> > ANGLE 0.0000 0.0001
> > 0.0000
> > DIHED 0.0000 0.0000
> > 0.0000
> > VDWAALS -18.2614 1.2729
> > 0.0900
> > EEL -7.0523 1.8874
> > 0.1335
> > 1-4 VDW -0.0000 0.0001
> > 0.0000
> > 1-4 EEL -0.0000 0.0000
> > 0.0000
> > EPB 23.2749 5.0209
> > 0.3550
> > ENPOLAR -13.9814 0.2315
> > 0.0164
> > EDISPER 22.1291 0.5543
> > 0.0392
> >
> > DELTA G gas -25.3137 2.2277
> > 0.1575
> > DELTA G solv 31.4226 5.0797
> > 0.3592
> >
> > DELTA TOTAL 6.1089 4.1135
> > 0.2909
> >
> >
> >
> >
> >
> >
> > On Thu, Jul 6, 2017 at 4:27 PM, Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> >> HI,
> >> I assume this delta G is the results of either PB or GB calculations.
> >> In the absence of entropy calculations, this delta G total reflects only
> >> the enthalpy component and hence not the true delta G binding.
> >>
> >> Best Regards
> >> Elvis Martis
> >> Mumbai, INDIA.
> >>
> >> ________________________________________
> >> From: NADIA RAHMAH <nadiiarah.apps.ipb.ac.id>
> >> Sent: 06 July 2017 12:45:40
> >> To: AMBER Mailing List
> >> Subject: [AMBER] MMPBSA Delta total results
> >>
> >> Hello Amber Users, I want to ask about MMPBSA results, at the end of the
> >> results, I get DELTA TOTAL :
> >>
> >> DELTA G gas -24.9391 2.2411
> >> 0.1585
> >> DELTA G solv 34.0352 3.5423
> >> 0.2505
> >>
> >> DELTA TOTAL 9.0961 3.7742
> >> 0.2669
> >>
> >> I want to ask, is DELTA TOTAL same with Delta G Binding? because I dont
> >> find Delta G Binding in my results. and the delta total value is so
> >> positive. Thanks
> >> --
> >>
> >> *Regards,*
> >> *Nadia Rahmah*
> >> *Department of Physics Undergraduate Student - 2013Bogor Agricultural
> >> University*
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> >
> > *Regards,*
> > *Nadia Rahmah*
> > *Department of Physics Undergraduate Student - 2013Bogor Agricultural
> > University*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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>
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>
--
*Regards,*
*Nadia Rahmah*
*Department of Physics Undergraduate Student - 2013Bogor Agricultural
University*
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Received on Thu Jul 06 2017 - 20:30:03 PDT
