| Run on Thu Feb 11 13:11:48 EST 2010 |Input file: |-------------------------------------------------------------- |sample input file for running alanine scanning | &general | startframe=1, endframe=50, interval=1, | verbose=1, mpi_cmd = "mpirun -np 2", nproc=2 |/ |&gb | saltcon=0.1 |/ |&pb | istrng=0.100 |/ |&alanine_scanning |/ |-------------------------------------------------------------- |Solvated complex topology file: ras-raf_solvated.prmtop |Complex topology file: rasraf.prmtop |Receptor topology file: ras.prmtop |Ligand topology file: raf.prmtop |Initial mdcrd(s): bigprod.mdcrd |Mutant complex topology file: rasraf_mutant.prmtop |Mutant receptor topology file: ras_mutant.prmtop |Mutant ligand topology file: raf.prmtop | |Best guess for receptor mask: ":1-166" |Best guess for ligand mask: ":167-242" |Calculations performed using 50 frames. |Poisson Boltzmann calculations performed using internal PBSA solver in sander. | |All units are reported in kcal/mole. ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- GENERALIZED BORN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1863.7944 17.1704 2.4283 EEL -17200.7297 75.9366 10.7391 EGB -3142.2247 63.1977 8.9375 ESURF 91.3565 1.3938 0.1971 G gas -19064.5240 77.8536 11.0102 G solv -3050.8682 63.2131 8.9397 TOTAL -22115.3922 51.5332 7.2879 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1268.1888 14.2342 2.0130 EEL -11557.0773 71.7127 10.1417 EGB -2444.8629 54.9156 7.7662 ESURF 64.2843 1.1143 0.1576 G gas -12825.2661 73.1118 10.3396 G solv -2380.5786 54.9269 7.7678 TOTAL -15205.8447 36.8422 5.2103 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -529.3090 9.4198 1.3322 EEL -4684.4720 36.1449 5.1117 EGB -1661.8286 26.5442 3.7539 ESURF 37.0493 0.6185 0.0875 G gas -5213.7811 37.3522 5.2824 G solv -1624.7794 26.5514 3.7549 TOTAL -6838.5604 25.6515 3.6277 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -66.2966 4.2751 0.6046 EEL -959.1803 34.9190 4.9383 EGB 964.4668 32.9201 4.6556 ESURF -9.9770 0.3759 0.0532 DELTA G gas -1025.4769 35.1797 4.9752 DELTA G solv 954.4898 32.9223 4.6559 DELTA G binding = -70.9871 +/- 6.6875 0.9457 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- I21A MUTANT: GENERALIZED BORN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1855.4226 17.0765 2.4150 EEL -17210.2882 75.8866 10.7320 EGB -3145.1010 63.2477 8.9446 ESURF 91.8639 1.3913 0.1968 G gas -19065.7108 77.7842 11.0003 G solv -3053.2370 63.2630 8.9467 TOTAL -22118.9478 50.9582 7.2066 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1261.9126 14.1817 2.0056 EEL -11566.4419 71.5475 10.1183 EGB -2447.4831 55.0008 7.7783 ESURF 64.5090 1.1105 0.1570 G gas -12828.3545 72.9394 10.3152 G solv -2382.9741 55.0120 7.7799 TOTAL -15211.3287 36.2055 5.1202 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -529.3090 9.4198 1.3322 EEL -4684.4720 36.1449 5.1117 EGB -1661.8286 26.5442 3.7539 ESURF 37.0493 0.6185 0.0875 G gas -5213.7811 37.3522 5.2824 G solv -1624.7794 26.5514 3.7549 TOTAL -6838.5604 25.6515 3.6277 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -64.2010 4.0841 0.5776 EEL -959.3742 34.9114 4.9372 EGB 964.2108 32.9092 4.6541 ESURF -9.6943 0.3800 0.0537 DELTA G gas -1023.5752 35.1495 4.9709 DELTA G solv 954.5164 32.9114 4.6544 DELTA G binding = -69.0588 +/- 6.5302 0.9235 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- RESULT OF ALANINE SCANNING: (I21A MUTANT:) DELTA DELTA G binding = 1.9283 +/- 9.3470 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- POISSON BOLTZMANN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1863.7944 17.1704 2.4283 EEL -17200.7297 75.9366 10.7391 EPB -3227.2145 64.4523 9.1149 ECAVITY 68.4754 0.7567 0.1070 G gas -19064.5240 6061.1875 857.1813 G solv -3158.7391 64.4568 9.1156 TOTAL -7522.2032 51.2973 7.2545 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1268.1888 14.2342 2.0130 EEL -11557.0773 71.7127 10.1417 EPB -2485.3559 54.5638 7.7165 ECAVITY 47.5088 0.4610 0.0652 G gas -12825.2661 5345.3320 755.9441 G solv -2437.8471 54.5658 7.7168 TOTAL -5118.8075 38.9610 5.5099 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -529.3090 9.4198 1.3322 EEL -4684.4720 36.1449 5.1117 EPB -1684.5802 28.2572 3.9962 ECAVITY 28.1687 0.3939 0.0557 G gas -5213.7811 1395.1865 197.3092 G solv -1656.4114 28.2599 3.9966 TOTAL -2313.4381 24.9082 3.5225 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -66.2966 4.2751 0.6046 EEL -959.1803 34.9190 4.9383 EPB 942.7215 33.8861 4.7922 ECAVITY -7.2022 0.3069 0.0434 DELTA G gas -1025.4769 1237.6138 175.0250 DELTA G solv 935.5194 33.8875 4.7924 DELTA G binding = -89.9575 +/- 8.2480 1.1664 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- I21A MUTANT: POISSON BOLTZMANN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1855.4226 17.0765 2.4150 EEL -17210.2882 75.8866 10.7320 EPB -3229.1405 64.8100 9.1655 ECAVITY 68.5521 0.7596 0.1074 G gas -19065.7108 6050.3755 855.6523 G solv -3160.5884 64.8144 9.1661 TOTAL -7520.1586 50.6710 7.1660 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1261.9126 14.1817 2.0056 EEL -11566.4419 71.5475 10.1183 EPB -2487.5603 54.6289 7.7257 ECAVITY 47.6466 0.4632 0.0655 G gas -12828.3545 5320.1609 752.3844 G solv -2439.9137 54.6309 7.7260 TOTAL -5118.8820 38.4370 5.4358 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -529.3090 9.4198 1.3322 EEL -4684.4720 36.1449 5.1117 EPB -1684.5802 28.2572 3.9962 ECAVITY 28.1687 0.3939 0.0557 G gas -5213.7811 1395.1865 197.3092 G solv -1656.4114 28.2599 3.9966 TOTAL -2313.4381 24.9082 3.5225 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -64.2010 4.0841 0.5776 EEL -959.3742 34.9114 4.9372 EPB 942.9999 34.0350 4.8133 ECAVITY -7.2632 0.3107 0.0439 DELTA G gas -1023.5752 1235.4872 174.7243 DELTA G solv 935.7367 34.0364 4.8135 DELTA G binding = -87.8385 +/- 8.0665 1.1408 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- RESULT OF ALANINE SCANNING: (I21A MUTANT:) DELTA DELTA G binding = 2.1190 +/- 11.5368 ------------------------------------------------------------------------------- -------------------------------------------------------------------------------