| Run on Thu May 20 12:26:23 EDT 2010 |Input file: |-------------------------------------------------------------- |Input file for running PB and GB |&general | endframe=50, verbose=1, |# entropy=1, |/ |&gb | igb=2, saltcon=0.100 |/ |&pb | istrng=0.100, |/ |-------------------------------------------------------------- |Complex topology file: ras-raf.prmtop |Receptor topology file: ras.prmtop |Ligand topology file: raf.prmtop |Initial mdcrd(s): prod.mdcrd | |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 16.9979 2.4039 EEL -17200.7297 75.1734 10.6311 EGB -3249.6511 64.5521 9.1290 ESURF 92.2130 0.9783 0.1383 G gas -19064.5240 77.0712 10.8995 G solv -3157.4381 64.5595 9.1301 TOTAL -22221.9622 50.4305 7.1319 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1268.1888 14.0912 1.9928 EEL -11557.0773 70.9920 10.0398 EGB -2532.0669 57.1203 8.0780 ESURF 64.4505 0.6125 0.0866 G gas -12825.2661 72.3770 10.2356 G solv -2467.6163 57.1236 8.0785 TOTAL -15292.8825 34.9738 4.9460 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -529.3090 9.3251 1.3188 EEL -4684.4720 35.7816 5.0603 EGB -1688.9631 26.2686 3.7149 ESURF 38.5996 0.5157 0.0729 G gas -5213.7811 36.9768 5.2293 G solv -1650.3635 26.2737 3.7157 TOTAL -6864.1445 25.6914 3.6333 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -66.2966 4.2321 0.5985 EEL -959.1803 34.5681 4.8887 EGB 971.3789 32.7175 4.6270 ESURF -10.8372 0.3827 0.0541 DELTA G gas -1025.4769 34.8262 4.9252 DELTA G solv 960.5417 32.7197 4.6273 DELTA G binding = -64.9352 +/- 6.2195 0.8796 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- POISSON BOLTZMANN: Complex: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1863.7944 16.9979 2.4039 EEL -17200.7297 75.1734 10.6311 EPB -3216.4580 65.8636 9.3145 ECAVITY 67.8762 0.7739 0.1094 G gas -19064.5240 77.0712 10.8995 G solv -3148.5819 65.8682 9.3152 TOTAL -22213.1059 51.7404 7.3172 Receptor: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -1268.1888 14.0912 1.9928 EEL -11557.0773 70.9920 10.0398 EPB -2489.5961 55.9347 7.9104 ECAVITY 47.1495 0.4689 0.0663 G gas -12825.2661 72.3770 10.2356 G solv -2442.4466 55.9367 7.9106 TOTAL -15267.7127 38.0230 5.3773 Ligand: Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -529.3090 9.3251 1.3188 EEL -4684.4720 35.7816 5.0603 EPB -1673.2571 27.4049 3.8756 ECAVITY 28.0328 0.4091 0.0579 G gas -5213.7811 36.9768 5.2293 G solv -1645.2243 27.4079 3.8761 TOTAL -6859.0053 24.7884 3.5056 Differences (Complex - Receptor - Ligand): Energy Component Average Std. Dev. Std. Err. of Mean ------------------------------------------------------------------------------- VDWAALS -66.2966 4.2321 0.5985 EEL -959.1803 34.5681 4.8887 EPB 946.3952 34.1668 4.8319 ECAVITY -7.3062 0.2973 0.0420 DELTA G gas -1025.4769 34.8262 4.9252 DELTA G solv 939.0890 34.1681 4.8321 DELTA G binding = -86.3878 +/- 8.1828 1.1572 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- WARNINGS: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi)