biosimspace
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An interoperable Python framework for biomolecular simulation.
It would be desirable to make it easier for users to combine molecules parameterised with openff-bespokefit with other system components. This would lower barriers for benchmarking studies with forcefield parameters...
Despite our package building against the correct version of `jaxlib`, i.e.: ``` jax: 0.4.19-pyhd8ed1ab_0 conda-forge jaxlib: 0.4.19-cpu_py39h45b9b01_0 conda-forge ``` when installing the Python 3.9 development version of BioSimSpace you end...
**Describe the bug** When using BSS.Parameters.parametrise() on a protein system, If BioSimSpace detects a disulfide bridge between cystein residues, it will add a "bond" command to the leap script: ![image](https://github.com/OpenBioSim/biosimspace/assets/31316943/a89ea151-f0f4-4410-b45b-dbd01884011e)...
Hello! I'm currently matching and merging molecules for MCL1 ligands. The basic code used to replicate these is: ```python # ligands lig0 = "lig_27" lig1 = "lig_42" # options prematch...
The current matchAtoms() uses the entire molecule to get MCS, a simple idea to accelerate it is to get MCS for heavy atoms and then match up hydrogens hanging off...
This PR introduces protein FEP functionality to BioSimSpace and allows for creating of hybrid protein/peptide systems with single or multiple simultaneous modifications, which can include point mutations to canonical or...