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choderalab
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Hi, I would calculate the hydration free energy of ethanol using OpenMM with CHARMM Drude force field but I don't know how to do that. My questions are: does Yank...
Hi, I was trying to run the setup-protein.sh with my own protein in the example folder "t4-lysozyme". Here's the error, Preparing receptor by adding missing atoms... Traceback (most recent call...
I'd like to use yank to calculate binding free energy for a peptide binding to a protein. I couldn't find any examples of this, so I'm not sure if this...
I have reviewed some previous issues and it appears that the problem I have run into is that our cluster is set up such that we cannot modify the GPU...
Recently, I've been reproduce the Freesolv result by YANK, I've encounterd lots of `NAN` in my experiments, here I'd like to conclude some solutions I've founded. 1. For some molecules,...
Hi, I am calculating the binding affinity of a small molecule sandwiched between two proteins. In the absence of the small molecule, these two proteins do not bind under physiological...
I am receiving errors when trying to generate the analyse report for a simulation where I imported the topology and structure files from Gromacs as per http://getyank.org/latest/tutorial.html#when-the-automatic-pipeline-won-t-do The files are...
Dear all. Recently, I have perform several yank tests, and encountered a problem in the end of yank calculation logs. There are two cases of yank's calculation results, one can...
Hi， I have read the readme file in yank benchmark c-Met_hinge_binders and noticed the follow comments: sams-twostage-boresch-dense.yaml - single-replica SAMS with dense alchemical protocol and Boresch restraints (experimental) sams-twostage-harmonic-dense.yaml -...
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An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.