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choderalab
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
I just changed the input files in the yank default yaml script. After running yank using amber prmtop and inpcrd files for 25 iterations , i got the following error....
Possibly precedes #1286, resolves https://github.com/choderalab/yank/issues/1270
A error was prompted in the following: 2022-09-08 11:27:09,197: Setting CUDA platform to use precision model 'mixed'. 2022-09-08 11:27:09,319: Single node: executing 2022-09-08 11:27:09,320: Running _setup_molecules serially. Traceback (most recent...
Hi all, just encountered an error when trying to install Yank 0.25.2 w/ python3.10: `class CombinatorialTree(collections.MutableMapping): AttributeError: module 'collections' has no attribute 'MutableMapping' ` Changing the import statements to `import...
Hello, I don't know if this is the proper place to ask this question but I am trying to calculate the free binding energy between an antibody and a pMHC...
Hi, thanks for the great project! I was a bit surprised to see that the examples here (and in the yank-examples repo) for hydration free energy include not one thermodynamic...
Hi everyone, I am estimating absolute free binding estimation of HDAC11 with its known ligand FT895. Here is my yank_ft895.yaml file: --- options: verbose: yes minimize: yes default_timestep: 2.0*femtoseconds default_nsteps_per_iteration:...
Hello Yank team, I am trying to run a benchmark using the data available here https://github.com/MCompChem/fep-benchmark . I have been running simulations with different samplers and end up with widely...
Hi, yank team, Does yank support membrane protein systems ? If this is possible, how to set it up ? Thanks for replying in advance!
Noting down YANK issues as I've been encountering them recently with the OpenMMTools API shift: I'm encountering another example where setup runs fine but during the propagation/mixing steps the following...
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An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.