Using path sampling to study ligand binding/unbinding kinetics
choderalab / ligand-binding-pathsampling Goto Github PK
View Code? Open in Web Editor NEWUsing path sampling to study ligand binding/unbinding kinetics
Using path sampling to study ligand binding/unbinding kinetics
@jhprinz : I've created a very basic attempt at ligand unbinding for a simple CB7:B2 host-guest system (using openmmtools >=0.8.0
):
https://github.com/choderalab/ligand-binding-pathsampling/tree/master/host-guest/cb7-b2
The current script dies with the error
[LSKI1497:ligand-binding-pathsampling/host-guest/cb7-b2] choderaj% python -i run-ops.py
Creating host-guest system...
Creating template...
Creating an integrator...
Selecting a platform...
Creating engine...
Creating a "hot" engine...
Initializing storage...
(store.engines[DynamicsEngine], 11, UUID('137432cf-5ab5-11e6-9087-000000000010'))
(store.engines[DynamicsEngine], 11, UUID('137432cf-5ab5-11e6-9087-000000000014'))
CPU
CPU
<openpathsampling.engines.openmm.topology.MDTrajTopology object at 0x119cf75d0>
Traceback (most recent call last):
File "run-ops.py", line 111, in <module>
storage.save([compute_contacts])
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/netcdfplus.py", line 617, in save
return [self.save(part, idx) for part in obj]
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/netcdfplus.py", line 628, in save
return store, store_idx, store.save(obj, idx)
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/objects.py", line 1371, in save
reference = super(UniqueNamedObjectStore, self).save(obj, idx)
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/objects.py", line 1183, in save
reference = super(NamedObjectStore, self).save(obj)
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/netcdfplus/objects.py", line 853, in save
self._save(obj, n_idx)
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/storage/stores/collectivevariable.py", line 18, in _save
self.add_diskcache(cv)
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/storage/stores/collectivevariable.py", line 96, in add_diskcache
chunksize=chunksize
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/storage/stores/snapshot.py", line 939, in add_cv
params = NetCDFPlus.get_value_parameters(cv(template))
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 231, in __getitem__
return self._post[items]
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 244, in __getitem__
return np.array(self._post[items])
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 277, in __getitem__
return self._post[[items]][0]
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 72, in __getitem__
rep = self._post[nones]
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 65, in __getitem__
results = self._get_list(items)
File "/Users/choderaj/miniconda/lib/python2.7/site-packages/openpathsampling-0.9.0-py2.7.egg/openpathsampling/chaindict.py", line 360, in _get_list
if self.scalarize_numpy_singletons and results.shape[-1] == 1:
AttributeError: 'tuple' object has no attribute 'shape'
Any ideas?
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ 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. ๐๐๐
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 โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.