There are differences (Complex - Receptor - Ligand) printed in both GB and
PB section. Value of "DELTA TOTAL" is the binding energy (it does not
include entropy). So there is no error in input/output files.
On Sun, Mar 23, 2014 at 7:01 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear Sir,
>
> I did run the command for MMPBSA as follow.
>
> 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
>
> I command run successfully but the net delta G is not calculated at the end
> of MMGBSA and MMPBSA calculation.
>
> Even I did calculate manually the energy value is positive.
>
> Here I am sending you the detail of the result.
>
> |
> |
> |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
>
>
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
> I request you to kindly guide me in debugging the error as to reason why
> the delta G value has not been calculated in the result. Moreover on
> manuall caculation of binding energy the value caomes to be positive.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
==================================================
Sushil Kumar Mishra, PhD
--------------------------------------------------
CEITEC- Central European Institute of Technology. MU
ILBIT, Building A4 - 2.12
Kamenice 5, Brno 625 00
Czech Republic
--------------------------------------------------
Email : sushil.chemi.muni.cz
Phone : +420-549 496 307
==================================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 23 2014 - 01:00:02 PDT
