search

CCPBioSim / fesetup

A tool for setting up free energy simulations.
http://www.ccpbiosim.ac.uk/software
GNU General Public License v2.0
34 stars 18 forks source link

Ligand correct_for_pH #13

Closed skfegan closed 4 years ago

skfegan commented 4 years ago

The options lig['correct_for_pH'] and lig['pH'] are not documented.

  1. check how/if they work
  2. fix any bugs
  3. add documentation
velocirraptor23 commented 4 years ago

It seems, there is the keyword in FESetup to setup pH for ligand but it seems desnt work. When I see the log file the pH for ligand is always 7.4. Is this meaningless term?

skfegan commented 4 years ago

The ligand correct_for_pH = true option also requires that add_hydrogens = true (add_hydrogens default is false). It will still need more testing.

skfegan commented 4 years ago

The ligand correct_for_pH and pH keywords work. Note: they are different to the propka and propka.pH keywords that are used for proteins. I would recommend that anyone using these keywords checks the output structures and charges to make sure they are suitable for the systems/conditions being studied.