cespos

Specify ions during system setup

15

**Is your feature request related to a problem? Please describe.** Hi! I could not find the option to specify the ions to use during system preparation, what in tleap would...

Add extra arguments to some functions

2

Hi! If possible, it would be helpful to have some extra arguments in "wrapper" functions. For example, while the Process functions `BioSimSpace.Process.Amber(), BioSimSpace.Process.Gromacs(), BioSimSpace.Process.OpenMM(), [...]` support the arguments `name, work_dir,...

Specify disulfide bridges during parameter file generation

17

**Is your feature request related to a problem? Please describe.** I have tried to prepare a system containing 4 disulfide bridges, however SS-bridge parameters were not in the output parameter...

Coupling groups in Gromacs

2

**Is your feature request related to a problem? Please describe.** Hi, I tried to use BSS to run MD simulations for a protein-ligand complex using Gromacs. Looking at the configuration...

[BUG] Protein parametrization fails if detects a disulfide bridge between reduced cysteine residues (CYS and not CYX)

2

**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: ...

Prepare systems with multiple ligands

9

**Is your feature request related to a problem? Please describe.** I was trying to prepare a system with a protein and 2 ligands (given as SDF files). However, both ligands...

ValueError: The filepath provided must end in `.keras` (Keras model format)

4

Hi! I have been trying to use AiZynthTrain to train AiZynthFinder with some personal reactions and reaction template. I have mapped and cleaned the reaction and template files with my...