Dear Sir
I followed the tutorial for MMGBSA and MMPBSA binding energy calculation.
Here the binding energy for MMGBSA comes to be negative whule for MMPBSA
comes to be positive.
I request you to kindly guide me as to how to include the entropy papramter
in the calculation of binding energy.
While going through the mailing list I got the following option
"To be comparable with the GB, you'll need to set inp=1, i.e. without
the EDISPER".
Here I dint get how to edit this parameter in mmpbsa.py file.
Here is what I have as mmpbsa.py file as given in the tutorial
Input file for running PB and GB in serial
&general
endframe=50, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
I request you to kindly guide me in debugging the error.
Here are the details of my input file and the output of FINAL_results
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
3pta-ZINC7587_solvated.prmtop -cp 3pta-ZINC7587.prmtop -rp 3pta.prmtop -lp
ZINC7587.prmtop -y *.mdcrd
| Run on Sat Mar 22 21:05:45 2014
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| endframe=50, keep_files=2,
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&pb
| istrng=0.100,
|/--------------------------------------------------------------
|MMPBSA.py Version=13.0
|Solvated complex topology file: 3pta-ZINC7271_solvated.prmtop
|Complex topology file: 3pta-ZINC7271.prmtop
|Receptor topology file: 3pta.prmtop
|Ligand topology file: ZINC7271.prmtop
|Initial mdcrd(s): density.mdcrd
| heat.mdcrd
|
|Receptor mask: ":1-904"
|Ligand mask: ":905"
|Ligand residue name is "UNK"
|
|Calculations performed using 50 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
-------------------------------------------------------------------------------
VDWAALS -7185.9660 37.9867 5.3721
EEL -60264.4859 183.3456 25.9290
EGB -12557.4149 150.1348 21.2323
ESURF 283.6370 2.5236 0.3569
G gas -67450.4518 177.9068 25.1598
G solv -12273.7779 148.2858 20.9708
TOTAL -79724.2297 63.2122 8.9396
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -7130.0858 36.3930 5.1468
EEL -60149.0804 184.4941 26.0914
EGB -12372.6935 151.4402 21.4169
ESURF 287.4385 2.5854 0.3656
G gas -67279.1662 181.1247 25.6149
G solv -12085.2550 149.4737 21.1388
TOTAL -79364.4213 63.1503 8.9308
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -4.2453 1.3481 0.1907
EEL -188.0198 5.0220 0.7102
EGB -135.5296 2.6845 0.3796
ESURF 4.8985 0.0265 0.0038
G gas -192.2651 5.2752 0.7460
G solv -130.6312 2.6796 0.3789
TOTAL -322.8962 4.0877 0.5781
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -51.6349 5.0840 0.7190
EEL 72.6143 8.4472 1.1946
EGB -49.1917 7.4061 1.0474
ESURF -8.7000 0.2032 0.0287
DELTA G gas 20.9795 8.1846 1.1575
DELTA G solv -57.8917 7.3822 1.0440
DELTA TOTAL -36.9122 4.1054 0.5806
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -7185.9660 37.9867 5.3721
EEL -60264.4859 183.3456 25.9290
EPB -12118.0713 124.8884 17.6619
ENPOLAR 7022.6122 17.9209 2.5344
EDISPER -3797.8137 15.2776 2.1606
G gas -67450.4518 177.9068 25.1598
G solv -8893.2728 120.6412 17.0612
TOTAL -76343.7246 81.5521 11.5332
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -7130.0858 36.3930 5.1468
EEL -60149.0804 184.4941 26.0914
EPB -11948.8780 127.1498 17.9817
ENPOLAR 7014.3938 18.0698 2.5555
EDISPER -3821.2696 15.7597 2.2288
G gas -67279.1662 181.1247 25.6149
G solv -8755.7538 123.1647 17.4181
TOTAL -76034.9201 81.0901 11.4679
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -4.2453 1.3481 0.1907
EEL -188.0198 5.0220 0.7102
EPB -125.4541 2.4403 0.3451
ENPOLAR 51.0216 0.2175 0.0308
EDISPER -52.6737 0.2364 0.0334
G gas -192.2651 5.2752 0.7460
G solv -127.1062 2.3689 0.3350
TOTAL -319.3713 4.5888 0.6489
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -51.6349 5.0840 0.7190
EEL 72.6143 8.4472 1.1946
EPB -43.7392 10.1252 1.4319
ENPOLAR -42.8032 0.5977 0.0845
EDISPER 76.1296 1.1474 0.1623
DELTA G gas 20.9795 8.1846 1.1575
DELTA G solv -10.4127 10.7266 1.5170
DELTA TOTAL 10.5668 6.4675 0.9146
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
Regards
Arunima
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Received on Sun Mar 23 2014 - 21:30:03 PDT
