Diogo

Hi, It's not yet supported in the GPU version, but it's likely it will be in the future. Best, On Tue, 30 Jun 2020 at 03:41, louetme wrote: > I...

Hi William, We have been developing a workflow for covalent docking in autodock-gpu, which involves preparing a flexible sidechain with [meeko](https://github.com/forlilab/Meeko). You'll need to `git clone` or download the meeko...

@vlkale I think you may be referring to the E50 plots, which are described in [J. Chem. Theory Comput. 2021, 17, 2, 1060–1073](https://doi.org/10.1021/acs.jctc.0c01006). See for example https://github.com/ccsb-scripps/AutoDock-GPU/pull/139#issuecomment-888633471.

After reading online it seems that GitHub actions supports GPU, while Travis doesn't. Another point in favor of GH actions is no need to give permissions to an external service.

@L30nardoSV definitely a good idea!

It's possible, but complicated, because the maps for each of the atom types have contributions from vdw, hbond, and desolv terms. 1. create four versions of the parameter file, which...

Hi @Hong-Rui, 1) I don't know. 2) Yes the LGA is different. 3) It's hard to tell because we haven't compared these programs explicitly for the case of flexible sidechains....

Genetic algorithms and simulated annealing are global search methods. The only global search method available in Autodock-GPU is a Lamarckian Genetic Algorithm (LGA), which is a genetic algorithm enhanced with...

Hi Eric, this is a good idea, we will consider it.

Hi, It's here: https://github.com/ccsb-scripps/AutoDock-GPU/blob/2ecd342b493d1e9b7b488ea2b642df1e0adcb50d/common/defines.h#L83 50 amino acids is too big for autodock. It's difficult to converge when the number of rotatable bonds is greater than 20. Furthermore, bond lengths and...