Dear Sir
Here while detlta G by MMPBSA for protein-ligand complex I am geting the
positive for delta G. Here one of the residue C1191 has been mutated to
C1191I and then the delta G binding have been calculated.
Here are the details of input command and the Final results
#!/bin/sh
#PBS -N C1191K_3781_r
#PBS -l select=1:ncpus=8
#PBS -j oe
#PBS -q small
cd $PBS_O_WORKDIR > pwd
cat $PBS_NODEFILE > pbsnodes
/opt/intel/impi/4.1.0.024/intel64/bin/mpirun -machinefile $PBS_NODEFILE -np
8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat
-sp C1191K_DRG_solvated.prmtop -cp C1191K_DRG.prmtop -rp C1191K.prmtop -lp
DRG.prmtop -y *.mdcrd
and final results is
| Run on Wed Apr 23 12:59:52 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: C1191K_DRG_solvated.prmtop
|Complex topology file: C1191K_DRG.prmtop
|Receptor topology file: C1191K.prmtop
|Ligand topology file: DRG.prmtop
|Initial mdcrd(s): prod1.mdcrd
| prod2.mdcrd
| prod3.mdcrd
| prod4.mdcrd
|
|Receptor mask: ":1-904"
|Ligand mask: ":905"
|Ligand residue name is "DRG"
|
|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 -7105.9549 37.1516
5.2540
EEL -60495.4331 136.2643
19.2707
EGB -13576.3408 108.7259
15.3762
ESURF 317.7194 2.3486
0.3321
G gas -67601.3880 132.5081
18.7395
G solv -13258.6214 108.5890
15.3568
TOTAL -80860.0094 76.4186
10.8072
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -7041.2146 36.8553
5.2121
EEL -60235.8628 136.4470
19.2965
EGB -13613.4078 109.1462
15.4356
ESURF 321.1359 2.3675
0.3348
G gas -67277.0774 133.0972
18.8228
G solv -13292.2719 108.9401
15.4065
TOTAL -80569.3493 76.4771
10.8155
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -4.9995 1.0120
0.1431
EEL -192.3961 5.0223
0.7103
EGB -50.3208 2.3839
0.3371
ESURF 4.7821 0.0367
0.0052
G gas -197.3956 5.0687
0.7168
G solv -45.5387 2.3822
0.3369
TOTAL -242.9343 3.5216
0.4980
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -59.7408 3.9526
0.5590
EEL -67.1741 7.3094
1.0337
EGB 87.3878 6.1042
0.8633
ESURF -8.1986 0.2427
0.0343
DELTA G gas -126.9150 7.4496
1.0535
DELTA G solv 79.1893 6.0356
0.8536
DELTA TOTAL -47.7257 3.3376
0.4720
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -7105.9549 37.1516
5.2540
EEL -60495.4331 136.2643
19.2707
EPB -12846.0437 104.1220
14.7251
ENPOLAR 7191.2844 13.3861
1.8931
EDISPER -4213.4735 16.1066
2.2778
G gas -67601.3880 132.5081
18.7395
G solv -9868.2328 104.5720
14.7887
TOTAL -77469.6208 83.4768
11.8054
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -7041.2146 36.8553
5.2121
EEL -60235.8628 136.4470
19.2965
EPB -12896.9755 105.5942
14.9333
ENPOLAR 7181.9466 13.5488
1.9161
EDISPER -4236.1658 16.5780
2.3445
G gas -67277.0774 133.0972
18.8228
G solv -9951.1947 106.1838
15.0167
TOTAL -77228.2721 83.3418
11.7863
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -4.9995 1.0120
0.1431
EEL -192.3961 5.0223
0.7103
EPB -50.2288 2.5536
0.3611
ENPOLAR 50.7049 0.2227
0.0315
EDISPER -53.3813 0.3485
0.0493
G gas -197.3956 5.0687
0.7168
G solv -52.9052 2.5927
0.3667
TOTAL -250.3008 3.5302
0.4992
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -59.7408 3.9526
0.5590
EEL -67.1741 7.3094
1.0337
EPB 101.1607 7.3105
1.0339
ENPOLAR -41.3671 1.2286
0.1737
EDISPER 76.0735 1.3057
0.1846
DELTA G gas -126.9150 7.4496
1.0535
DELTA G solv 135.8671 7.3979
1.0462
DELTA TOTAL 8.9521 5.0649
0.7163
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
I request you yo kindly guide me in debugging the error.
Regards
Arunima
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Received on Wed Apr 23 2014 - 20:30:03 PDT
