Hello everyone,
I calculated binding affinity of a ligand using thermodynamic integration
method in both water as well as protein environment for charge annihilation
and Vdw decoupling steps.
The RMSF of DV/DL value coming out to be very high hence the +- variance,
also the final energy is coming out -16.66 (which is nt expected). All the
calculations are done using The trapezoid rule as in the tutorial
http://ambermd.org/tutorials/advanced/tutorial9/
All details of the chosen lambda values and calculation is pasted below
*Ligand_Water* *
* *
* *Protein_Ligand_Water*
*Charge Annihilation* *
* *
* *Charge Annihilation*
Lambda Values DV/DL RMS
Lambda Values DV/DL RMS
difference sqr of first sqr of second Sum of first and second sqrt of Sum
l: 0.00 (w=0.025) cont: -14.4890+-1.8476
0.05 2716.212 48.1331
0.05 3219.558 56.0805
-503.3466 2316.795316 3145.02248 5461.817796 73.90411217
l: 0.05 (w=0.100) cont: -50.3347+-7.3904
0.2 2220.92 41.7418
0.2 2495.63 49.4251
-274.7098 1742.377867 2442.84051 4185.218377 64.69326377
l: 0.20 (w=0.225) cont: -61.8097+-14.5560
0.5 1378.454 40.4243
0.5 1350.787 45.4072
27.6672 1634.12403 2061.813812 3695.937842 60.7942254
l: 0.50 (w=0.250) cont: 6.9168+-15.1986
0.7 831.0057 40.6745
0.7 650.9688 44.8659
180.0369 1654.41495 2012.948983 3667.363933 60.5587643
l: 0.70 (w=0.200) cont: 36.0074+-12.1118
0.9 288.3239 40.7373
0.9 -64.8476 45.0639
353.1715 1659.527611 2030.755083 3690.282695 60.74769703
l: 0.90 (w=0.150) cont: 52.9757+-9.1122
0 0 0 0 0
l: 1.00 (w=0.050) cont: 21.9869+-3.0374
0 0 0 0 0
Total DV/DL:-8.74649166666665+-63.2538469855 -8.75 -63.25
0 0 0 0 0
0 0 0 0 0
*Ligand_Water* *
* *
* *Protein_Ligand_Water*
0 0 0 0 0
*Vdw_decoupling* *
* *
* *Vdw_decoupling*
0 0 0 0 0
Lambda Values DV/DL RMS
Lambda Values DV/DL RMS
#VALUE! #VALUE! #VALUE! #VALUE! #VALUE!
l: 0.00 (w=0.025) cont: -0.2909+-0.2479
0.05 26.1765 6.2411
0.05 34.1194 7.7044
-7.9429 38.95132921 59.35777936 98.30910857 9.915094985
l: 0.05 (w=0.050) cont: -0.3971+-0.4958
0.1 25.7989 6.346
0.1 30.0476 7.3311
-4.2487 40.271716 53.74502721 94.01674321 9.696223142
l: 0.10 (w=0.075) cont: -0.3187+-0.7272
0.2 24.7159 6.818
0.2 34.1307 8.8127
-9.4148 46.485124 77.66368129 124.1488053 11.14220828
l: 0.20 (w=0.100) cont: -0.9415+-1.1142
0.3 23.3889 7.3632
0.3 26.1398 8.0608
-2.7509 54.21671424 64.97649664 119.1932109 10.91756433
l: 0.30 (w=0.100) cont: -0.2751+-1.0918
0.4 21.3828 8.2142
0.4 30.6779 10.2335
-9.2951 67.47308164 104.7245223 172.1976039 13.12240846
l: 0.40 (w=0.100) cont: -0.9295+-1.3122
0.5 17.7962 9.6601
0.5 25.4745 11.5524
-7.6783 93.31753201 133.4579458 226.7754778 15.0590663
l: 0.50 (w=0.100) cont: -0.7678+-1.5059
0.6 10.7982 12.1569
0.6 10.7391 12.3487
0.0591 147.7902176 152.4903917 300.2806093 17.32860668
l: 0.60 (w=0.100) cont: 0.0059+-1.7329
0.7 -3.5089 16.518
0.7 8.8538 17.099
-12.3627 272.844324 292.375801 565.220125 23.77435856
l: 0.70 (w=0.100) cont: -1.2363+-2.3774
0.8 -49.5154 24.7586
0.8 2.3148 18.9386
-51.8302 612.988274 358.67057 971.6588439 31.17144276
l: 0.80 (w=0.100) cont: -5.1830+-3.1171
0.9 -37.8209 9.5618
0.9 -36.9657 9.6891
-0.8552 91.42801924 93.87865881 185.3066781 13.61273955
l: 0.90 (w=0.100) cont: -0.0855+-1.3613
l: 1.00 (w=0.050) cont: 2.5060+-0.6806
Total DV/DL:-7.913545+-15.764325329025
-7.91 -15.76
*-16.66* *-79.01*
Any suggestion will be highly appreciated
Thanks in advance
--
--
SUNITA GUPTA
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Received on Tue Oct 05 2010 - 00:30:03 PDT
