-
Dear Dr Fu,
Does BFEE support alchemical calculations of ligands with a nonzero net charge? I read that having a charge perturbation can lead to artifacts which require correction terms. Does BFEE2 c…
-
We use PARITY similarity to compare ligands within an EC class for a bound entity. Finding the most similar cognate ligands to a cognate ligand would also be useful - however could prove to be a very …
-
I have a series of 376 small molecules that I am trying to dock into a kinase structure. I set up a csv to run the complex in batch mode, following the template provided in the examples directory, as …
-
### Describe the bug
CUDA runtime error on example screening test case mmp13 (both v1.1.1 and v1.1.0. It was OK in v1.0).
The last log as follow:
```
Performing docking (random seed: 5) ... …
-
I tried to calculate an edge that does not have a perfect mapping and got two error messages. Can you please explain the meaning behind them? What exactly is the issue here?
- 0_easy_rbfe_A_complex…
-
I would like to ask if Vina-GPU-2.0 can perform Multiple ligands docking like Vina? if Yes, how to write the config file or submit the job?
I have tried to do it like Vina:
Vina-GPU2.0+ --config co…
-
Hello! I'm going to be running a benchmark with the p38, mcl1 and tyk2 ligands. Looking at the ligands available in this repo, I've noticed that some of the ligands are not included when compared to t…
-
It's a good job, but I got pre_lig_pos NAN when I used the pretrained ckpt to sampling ligands. Could you please check the sampling code?
-
I am running AToM for ABFE for my systems. I adapted the control script from the tutorial and I am trying it on different ligands (more than 20 heavy atoms) bound to the same protein. For some of them…
-