yank

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Hi there, I just wanted to let everyone know about a silent failure mode that I found recently. If you're using GAFF2 to parameterize the ligand, we know that you...

simonaxelrod

Hello yank team, I'm working on incorporating yank into a virtual screening pipeline. However, I had two questions. - How do I measure the total amount of simulation time used...

sammun-insitro

support for python 3.10?

2

Will yank support python 3.10? I'm running into errors when running the yank analysis notebook with the CLI using python 3.10. The first error I get: ``` Traceback (most recent...

zhang-ivy

problem during absolute binding energy calculation

3

Hi, When I run the absolute calculation protocol, I got the error below `subprocess.CalledProcessError: Command '['tleap', '-f', 'leap.in']' returned non-zero exit status 31.` I think that the subprocess error related...

mayank-kohli

Just wanted to report an issue + solution @ijpulidos helped me fix - noting it here for any future updates. **Problem:** Basically anytime I run something in YANK (after installing...

sukritsingh

I got the following error.

6

Hi, When i tried to the yank-example file. I got the following error. 2023-03-17 15:28:45,037: Running _compute_replica_energies serially. Traceback (most recent call last): File "/home/medicina/anaconda3/envs/fep/lib/python3.7/site-packages/openmmtools/cache.py", line 445, in get_context context...

VirtualChemist

pymbar 4 compatibility

1

I saw that there was a patch made in July to pin to pymbar 3 (https://github.com/choderalab/yank/pull/1285) - Are there plans to also support pymbar 4?

j-wags

getting the following error when running ``` yank analyze report --store=experiments --output=yank_output.ipynb --format ipynb ```: ``` Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. Rendering notebook as a .ipynb file......

RishalAggarwal

Hi, I am computing free energy of solvation for charged ligand in implicit water. I am curious to know how charged neutrality is enforced in vacuum. I am getting FES...

moradza

Failure to set up a single molecule terminates entire MPI calculation

1

I'm working on adding an example to set up and run the entire FreeSolv set (in [this branch](https://github.com/choderalab/yank-examples/tree/freesolv/examples/hydration/freesolv)), and noticed that this molecule takes out the entire calculation: ``` @MOLECULE...

jchodera