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?
2. The entropy DELTA S = -13.9278 is (298xDELTA S) .. ?
3. The DELTA Htotal = -258.2523 - 13.9278 = -272.1801 .. ?
4. The DELTA Gsol and DELTA Gpolar, I will get from the decompose file, the average submission of Polar and Non polar data.. ?
I had gone through the manual, I find some setails but I am confused to make any conclusion.
Sorry for silly question, but I am puzzled about this.
Thanks in advance
Abhi
On Fri, Apr 17, 2015 at 11:30 AM, Abhishek TYAGI <atyagiaa.connect.ust.hk>
wrote:
> Dear Jason,
>
> Thanks for your reply, the program is successfully running, now I am
> running for 30000 frames. As my input files generated from NAMD, i don't
> think that I can use nmode analysis, as it shows error while computing
> entropy, is it available in Ambertool or with the purchase version of Amber.
>
?normal mode calculations are not available with chamber topologies. If
you used amber files in NAMD, then you can do all parts of MMPBSA.py.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
------------------------------
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Received on Thu Apr 23 2015 - 01:00:02 PDT
