Steering water bridges - Githubissues

CBDD / openduck

Open-source DUck (Dynamic Undocking)

http://www.ub.edu/bl/undocking/

Apache License 2.0

7 stars 3 forks source link

Steering water bridges #17

Closed AlvaroSmorras closed 1 year ago

AlvaroSmorras commented 1 year ago

Added the following features:

Option to restraint water molecules from the waters_to_retain.
Option to use a water from water_to_retain pdb as the anchor point to steer from. If this option is enabled, that water is restrained by default.
Added multiprocessing to jarzynski bootstrap calculations to quicken it

AlvaroSmorras commented 1 year ago

Last commit changes the selection of atoms to perform the steering, to filter for 'good' atoms that perform the HB, even if they are not the closest. This might be problematic if the closest 'good' atom is far, which comes from a bad docking pose or something similar. I don't know if it should be hardcoded only to allow N and O, or it is better to add a new flag. The parser is becoming quite busy with so many options.

The water-bridge steering was been tested and seems to be working just fine