Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

How to Disable Desolvation Parameters in AutoDock Scoring Function during Docking? #253

Open
samdani1593 opened this issue Jan 22, 2024 · 3 comments
Labels
enhancement New feature or request

Comments

@samdani1593
Copy link

Hello,

I am currently working on a docking project using AutoDock, and I would like to switch off the desolvation parameters in the scoring function. I have reviewed the AutoDock documentation, but I couldn't find clear instructions on how to achieve this.

The Autodock version trying to implement: 4.2.6

If there are code modifications required, could you please guide me through the changes?

@rwxayheee
Copy link
Collaborator

rwxayheee commented Jan 22, 2024

Hi @samdani1593
Have you tried to include a custom parameter file in your DPF?
According to the AutoDock4 Manual pp. 39, you could point AutoDock4 to a modified parameter file. According to the documentation here, you could set FE_coeff_desolv to 0 in the modified parameter file.

@diogomart
Copy link
Member

There's two categories of interacting atom pairs:

  1. between static (receptor) and movable atoms (ligand and flexible sidechain)
  2. between movable atoms

For the first, which is arguably the most important one, desolvation needs to be disabled in autogrid, by the means that @rwxayheee explained: passing a modified parameter file with FE_coeff_desolv set to zero. This will disable dissolvation between the static atoms (receptor) and the moving atoms (ligand and flexible sidechains).

The second category of interactions, which are pairs of movable atoms, can't be disabled in AutoDock-GPU. DPF files are not fully supported, and the parameter_file keyword is ignored. It can be disabled in Vina with the command line option --weight_ad4_dsolv. The autogrid modification is still required for vina, because vina reads autogrid maps when using the AD4 scoring function.

@atillack
Copy link
Member

Although AD-GPUs atom types are currently fixed along with the corresponding coefficients (corresponding to AD4.1_bound.dat from AD4.2.6) changing them based on user input is something we did think about but haven't found the time to actually do ...

Now with the first user feedback this may be needed, I will turn this into a feature request.

@atillack atillack added the enhancement New feature or request label Jan 24, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

4 participants