Amber, FEP, hydration free energies

Can be done with Amber.
It requires calculations of the molecule in water and in vacuum.

There is an example calculation from Pär S in /temp2/Ulf/Finished/Fep-solv-e.
It employs the old sander version and divides into electrostatic and van der Waals parts.
It gives absolute hydration free energies.
The file shows how to set up the calculation.
Majda tried this approach for the Hyp project.

We tried to do relative solvation free energies the same way as binding free energies (in the Hyp project), but got problems to converge the vacuum part.
With Pär's approach, we got reasonable results.

We also tested to calculate the hydration free energies by COSMO. It turned out that many snapshots from MD is needed, ~10. Clustering may also be needed, but sampling is more important (to get an error estimate). Such calculations are fast.