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insilichem / gaudi

GaudiMM: A modular optimization platform for molecular design
http://gaudi.readthedocs.io
GNU Lesser General Public License v3.0
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Is there some doc on how to do protein-ligand docking with gaudi? #1

Closed UnixJunkie closed 4 years ago

UnixJunkie commented 7 years ago

Thanks!

jaimergp commented 7 years ago

Hi! Congrats on posting the very first issue!

The docs are hosted at ReadTheDocs and include a chapter on how to face different kind of problems with GaudiMM. Additionally, the Supporting Information contains the input files for the examples commented in the JCC paper.

Please ask any further doubt you may have!

UnixJunkie commented 7 years ago

A running example would be nice. Like something you can run with 'make dock_test'. People don't like to write a config file by hand from scratch; it is better if there is a correct template that just needs to be tweaked a little.

jaimergp commented 7 years ago

Well, the examples directory does contain a sample input file which contains all available genes and objectives, with all the parameters, both optional and compulsory. You can tailor an input file from that one just by stripping the unneeded blocks.

I'd start with two Molecule genes (Ligand and Protein), and a Search and Torsion genes applied on the Ligand. For the evaluation part, just use Clashes minimization and HBonds maximization and see what happens.

I'll upload a zip file with a runnable example shortly.

jaimergp commented 7 years ago

Hi!

This zip contains the files needed to run a docking test for the system 1VRH. Unzip it and run it with gaudi run docking_1vrh.yaml from the terminal. Let me know if this is enough!

gaudi-docking-test.zip

UnixJunkie commented 7 years ago

if it runs for you, then it is a good enough example and should be added to the corresponding directory. I looked the YAML file. There are several magic numbers (constants I don't know where they come from / what they mean) but it looks understandable.

jaimergp commented 7 years ago

Hi, thanks for the review.

Most of the core functions of GaudiMM are self-documented (if not all), but I understand that accessing the API documentation is not very straight-forward. Anyway, all the 'magic numbers' (or default config values) are discussed in the gaudi.parse.Settings class docstring:

http://gaudi.readthedocs.io/en/latest/api/gaudi.html#gaudi.parse.Settings

jotjot commented 5 years ago

Thank you!!! I was looking for such an example as well.

UnixJunkie commented 4 years ago

In the docking example, is the binding site described by a 12A sphere centered on the ligand?

UnixJunkie commented 4 years ago

A sphere with explicit center and radius is OK. A 3D point with allowed +/- dx, dy and dz is also standard.

jaimergp commented 4 years ago

In the docking example, is the binding site described by a 12A sphere centered on the ligand?

If memory serves, yes! More info: https://gaudi.readthedocs.io/en/latest/api/gaudi.genes.html#module-gaudi.genes.search

UnixJunkie commented 4 years ago

ok, thanks for the info