On Thu, Apr 23, 2015 at 3:56 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk>
wrote:
> Dear Jason,
>
>
> Thank you again for the valuable suggestion.
>
> I had successfully finished MMGBSA calculations, I got results in the form
> of Final_decomp.dar and Final_results.dat these results include
> decomposition results and quasi harmonic entropy calculations as follows:
>
> |Input file:
> |Input file for running PB and GB
> |&general
> |
> | startframe=1, endframe=50000, verbose=2, keep_files=2,
> strip_mask=":WAT:SOD:CLA", interval=2,
> | entropy=1,
> |/
> |&gb
> | igb=1, saltcon=0.100,
> |/
> |&decomp
> | idecomp=1, print_res="1-647",
> | dec_verbose=1,
> |/
> |--------------------------------------------------------------
> |MMPBSA.py Version=14.0
> |Solvated complex topology file: solvated.prmtop
> |Complex topology file: complex.prmtop
> |Receptor topology file: receptor.prmtop
> |Ligand topology file: ligand.prmtop
> |Initial mdcrd(s): last50-100ns.dcd
> |
> |Receptor mask: ":22-3957"
> |Ligand mask: ":1-21"
> |
> |Calculations performed using 25000 complex frames.
> |
> |Generalized Born ESURF calculated using 'LCPO' surface areas
> |
> |All units are reported in kcal/mole.
> |All entropy results have units kcal/mol (Temperature is 298.15 K).
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
> ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
> Translational Rotational Vibrational Total
> Complex: 17.4129 19.2593 2130.1008 2166.7729
> Receptor: 17.3037 19.2196 1424.6230 1461.1464
> Ligand: 15.4966 15.6526 688.4051 719.5543
>
> DELTA S: -15.3875 -15.6129 17.0727 -13.9278
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> GENERALIZED BORN:
>
> Complex:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND 1368.3544 25.2154
> 0.1595
> ANGLE 897.2118 18.7146
> 0.1184
> DIHED 1692.7552 24.5266
> 0.1551
> UB 1419.2579 13.7413
> 0.0869
> IMP 11.5122 2.0615
> 0.0130
> VDWAALS -2550.2458 17.4302
> 0.1102
> EEL 3300.6977 102.1449
> 0.6460
> 1-4 VDW 16821.6603 23.5359
> 0.1489
> 1-4 EEL -1468.3795 20.7275
> 0.1311
> EGB -5583.6608 96.4942
> 0.6103
> ESURF 70.5932 1.1135
> 0.0070
>
> G gas 21492.8243 114.0895
> 0.7216
> G solv -5513.0676 96.3799
> 0.6096
>
> TOTAL 15979.7567 49.7067
> 0.3144
>
> Receptor:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND 1185.6011 22.6463
> 0.1432
> ANGLE 521.4371 11.8407
> 0.0749
> DIHED 1004.1771 23.1426
> 0.1464
> UB 1277.0211 11.8346
> 0.0748
> VDWAALS -1971.1570 0.7240
> 0.0046
> 1-4 VDW 16450.8340 21.6077
> 0.1367
> ESURF 45.4089 0.1084
> 0.0007
>
> G gas 18467.9134 43.9488
> 0.2780
> G solv 45.4089 0.1084
> 0.0007
>
> TOTAL 18513.3223 43.9558
> 0.2780
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND 182.7533 11.2009
> 0.0708
> ANGLE 375.7747 14.4873
> 0.0916
> DIHED 688.5781 7.9904
> 0.0505
> UB 142.2368 7.0494
> 0.0446
> IMP 11.5122 2.0615
> 0.0130
> VDWAALS -221.2518 9.3618
> 0.0592
> EEL 3300.6977 102.1449
> 0.6460
> 1-4 VDW 370.8263 9.3341
> 0.0590
> 1-4 EEL -1468.3795 20.7275
> 0.1311
> EGB -5676.9577 95.4697
> 0.6038
> ESURF 32.8242 1.2398
> 0.0078
>
> G gas 3382.7479 98.8370
> 0.6251
> G solv -5644.1335 95.5106
> 0.6041
>
> TOTAL -2261.3856 19.0576
> 0.1205
>
> 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
> UB -0.0000 0.0001
> 0.0000
> IMP 0.0000 0.0000
> 0.0000
> CMAP 0.0000 0.0000
> 0.0000
> VDWAALS -357.8370 12.4921
> 0.0790
> EEL 0.0000 0.0000
> 0.0000
> 1-4 VDW -0.0000 0.0000
> 0.0000
> 1-4 EEL 0.0000 0.0000
> 0.0000
> EGB 93.2969 2.5730
> 0.0163
> ESURF -7.6400 0.4823
> 0.0031
>
> DELTA G gas -357.8370 12.4921
> 0.0790
> DELTA G solv 85.6569 2.5202
> 0.0159
>
> DELTA TOTAL -272.1801 11.4958
> 0.0727
>
> -------------------------------------------------------------------------------
>
>
> -------------------------------------------------------------------------------
> Using Quasi-harmonic Entropy Approximation: DELTA G binding = -258.2523
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> My questions are:
>
> 1. The entropy calculated here is -13.9278, Final binding energy is
>
> DELTA G binding = -258.2523 , is this correct?
>
Yes.
> 2. The entropy DELTA S = -13.9278 is (298xDELTA S) .. ?
>
Yes.
> 3. The DELTA Htotal = -258.2523 - 13.9278 = -272.1801 .. ?
>
DELTA G total, but yes.
>
> 4. The DELTA Gsol and DELTA Gpolar, I will get from the decompose file,
> the average submission of Polar and Non polar data.. ?
>
Actually DELTA Gsol and DELTA Gpolar are not really decomposable terms.
You they are computed via the PB or GB equations. I'm not sure what your
question is really trying to ask -- these values are the average
contributions from every snapshot computed for the entire system.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 23 2015 - 04:00:04 PDT
