P38 lig_p38a_2ff (present twice): Decide which rotamer to use

[hannahbaumann]

Ligand lig_p38a_2ff is deposited with two orientations of the cyclohexyl ring. Would it make sense to see whether one of them is more favorable and only include that one or to see if the conformations interconvert in MD?

[hannahbaumann]

Removed one configuration in commit f881ed302df025a8cd0bc5934ec3950610fd6e1d Kept the configuration that was more similar to the one in the old PLB (Hahn et al) and in the dataset from Schrodinger.

[hannahbaumann]

I noticed that for some ligands in this dataset, the conformation of the unsaturated ring is different from some of the other ligands/from the conformation in the old PLB. This can potentially lead to convergence problems. We could run an A-->B; B-->A tranformations for such a ligand pair to see whether there is slow convergence/whether the conformation has an impact on the DDG.