Comments (3)
This is now fixed. The problem was introduced when closing issue #46, i.e. adding a molecule to a list of molecules now extends the list, rather than creating a System object. (Previously, any multi-molecule data structure was converted to a System.) I've updated _solvent.py
to reflect the changes.
I'll also have to update the binding_freenrg.py
script used for the D3R2018 challenge as it will no longer work, i.e. the line...
system = merged + protein + waters
...will no longer create a system, but a list of molecules instead. We'll probably need to rethink this, as there is currently no way for the user to create a system from a list of molecules. (The System
object is deliberately hidden from the user and is only used internally.)
from biosimspace.
Thank you!
from biosimspace.
No problem.
To get around the other issue I'll create a MoleculeList
object that is subclassed from a regular Python list. I can then add a toSystem
method that converts the MoleculeList
to a system. Just noting here so I don't forget :-)
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Related Issues (20)
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- Absolute Binding Free Energy Calculations with GROMACS HOT 7
- Pickling a parametrised molecule from an SDF file with GAFF2 HOT 4
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- [BUG] OSError "It looks like you failed to include a topology file." when reading SDF which doesn't contain redundant bond order information HOT 10
- [BUG] Cannot import BioSimSpace after installation of biosimspace 2023.1.2 using mamba HOT 3
- AnalysisError: SOMD free-energy analysis failed! HOT 5
- [BUG] HOT 10
- Reporting a vulnerability
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- Issue in reproducing the funnel methadynamics tutorial HOT 2
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