Hi, It was my first attempt to use MM_PBSA. In MM_PBSA script, I
used GB program for solvation energy calculation, and my system includes
207 res and about 300 wat(solvatecap). The belows is the result of
MM_PBSA.
------------------------------------------------------------------------------
Complex (AB) Receptor (A) Ligand (B)
Contribution ----------------------- ------------------------------------
mean std mean std mean std
--------------------------------------------------------------------------
Eele -7125.1719 19.5950 -7131.1970 19.4149 55.4103 1.7476
EvdW 709.6931 209.5975 725.9703 209.2015 6.5952 1.4115
Einter 2433.0899 20.8501 2403.6254 20.2172 29.4646 3.9879
Egas -3982.4187 209.1412 -4001.6013 208.8900 91.4594 4.0415
E(nonp) 54.3154 0.1371 54.7697 0.1353 3.5090 0.0209
E(nonpGB) 70.9311 0.1821 71.5346 0.1797 3.4393 0.0278
E(GB) -1207.5667 16.0135 -1217.2146 15.9862 -22.1748 1.0877
E(sol) -1136.6355 15.9617 -1145.6799 15.9395 -18.7356 1.0818
E(GB+ele) -8332.7386 15.7243 -8348.4115 15.1948 33.2354 1.1136
E(tot,GB) -5119.0542 209.0189 -5147.2812 208.7454 72.7239 3.6919
---------------------------------------------------------------------
Interactions [AB-(A+B)]
------------------------------------
Contribution mean std
------------------------------------
Eelectrostat -49.3852 4.5673
EvdW -22.8723 4.2184
Egas -72.2768 3.8228
E(nonpolar) -3.9633 0.0399
E(nonpolGB) -4.0428 0.0530
E(GB) 31.8228 2.5724
E(solvation) 27.7800 2.5821
E(GB+elect) -17.5625 3.3003
E(total,GB) -44.4969 2.8664
-----------------------------------
Though there are a couple of emails on the list talking about meaning of
each items, I am still not clear what is the exact meaning for
the terms Egas and Einternal, and where them come from.
Secondly, it looks weird that the std values of Evdw and Egas for complex
and receptor are much larger than the others. Is there something wrong with my
computation?
The last question is which program, delphi or GB generally gives better
solvation energy?
Can anyone help me with those? Thanks a lots.
Xiaojian Tan
Received on Mon May 20 2002 - 16:04:52 PDT
