Research:GK FEP BAR
Simulation process and the parameters
The execuable for GK/Bar simulaton is located at: /users/jzhen/tinker5.1-gk-param/source4/
With RESPA multi-step implement (from Tinker6): /users/jzhen/tinker5.1-gk-param/source4-respa/
Relative binding free energy calculation: two states
bound state: protein-ligand in GK solvent
free state: ligand only in GK solvent
In each state, we scale ele first, and then vdW. A example of prameter and key file can be seen at: /users/jzhen/OSRW_GK/GK-bar/lig-pro/lig2-pro/. The ele is scaled from 1.0 to 0 by ele6 --> ele5 -->....ele2 --> ele1 --> vdw6, vdW is scaled from 1.0 to 0 (the well depthe psilon is scaled to 0.0 and the radious is scaled to 0.0001). For each windows, the simulation time is 150ps, timestep is 1.5fs with rattle and 3fs with respa/rattle
Solvation energy comparison
| Ligand | Published Label | PB (published result) |
PB-polar (published) |
GK (min structure) | PB (min structure) | PB (gas-min struct, tinker10-08) | PB (gas-min struct, tinker10-08, polar) | GK-FEP |
| Lig 1 | A | -54.2 | -56.8 | -61.0707 | -53.4881 | -54.9396 | -56.0900 | -60.7210 |
| Lig 2 | B | -55.6 | -58.1 | -63.0336 | -54.8510 | -57.2422 | -57.2155 | -62.9246 |
| Lig 3 | C | -58.3 | -60.9 | -66.6569 | -58.7613 | -60.1055 | -59.9958 | -66.5370 |
| Lig 6 | D | -53.4 | -56.2 | -59.1056 | -53.1730 | -54.3039 | -55.2043 | -58.6448 |
| Lig 4 | E | -57.6 | -60.1 | -55.5956 | -56.4508 | -57.9430 | -59.6392 | -55.4094 |
| Lig Yue | -- | -62.5264 | -57.8351 | -58.6675 | -59.0935 | -60.4647 |
- PB (published) vs GK
Directories
- /home/wuch/work/research/trypsin-ligand
- lig1,lig2,lig3,lig4,lig6,lig_yue
Questions
- Why are some torsion parameters different between the two?
- /home/oscar/trypsin/lig2/lig-pro/vdw1/vdw1.prm
- /home/oscar/trypsin/lig2/lig-pro/amoeba.prm