Examples for MHC-peptide free energy calculations using YANK
choderalab / mhc Goto Github PK
View Code? Open in Web Editor NEWExamples for MHC-peptide free energy calculations using YANK
License: MIT License
Examples for MHC-peptide free energy calculations using YANK
License: MIT License
I'm able to run other Yank examples (t4-lysozyme), but for this example I get an error that has something to do with the ligand resname. It appears to be trying to open the ligand as a mol2 file, but it's a peptide in PDB format. I am also running into the same error when I try to modify the t4-lysozyme example to use a peptide ligand.
2020-01-28 09:44:23,673: Setting CUDA platform to use precision model 'mixed'.
2020-01-28 09:44:23,772: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases
2020-01-28 09:44:23,813: Setting up the systems for mhc and peptide using solvent pme
Traceback (most recent call last):
File "run_yank.py", line 150, in
main(args.yaml_script_path, args.job_id, args.n_jobs)
File "run_yank.py", line 138, in main
experiment_builder.run_experiments()
File "/home/comer/anaconda3/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 751, in run_experiments
completed[exp_index] = self._run_experiment(exp, write_status=write_status)
File "/home/comer/anaconda3/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 3247, in _run_experiment
built_experiment = self._build_experiment(experiment_path, experiment)
File "run_yank.py", line 126, in _build_experiment
experiment = super(TwoRestraintsBuilder, self)._build_experiment(*args, **kwargs)
File "/home/comer/anaconda3/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 3042, in _build_experiment
ligand_resname = utils.Mol2File(ligand_descr['filepath']).resname
File "/home/comer/anaconda3/envs/yank/lib/python3.7/site-packages/yank/utils.py", line 1124, in resname
return next(self.resnames)
StopIteration
Current DSL strings in the .yaml files to identify ligand in both complex and solvation experiments are highly specific. A more general way is needed to demarcate ligands to increase automated throughput.
Attempting to run PDBFixer with keepIds=True leads to instability during subsequent short OpenMM simulation, with error message "Particle coordinates are NaN."
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.