insukjoung

Solvation issues and enhancements

6

Hi, First of all, thank you for sharing your precious source code. I am having trouble in topology generation regarding solvation. https://github.com/luancarvalhomartins/PyAutoFEP/blob/fcc52e914fac9edebc1675dd032421915a2986f4/prepare_dual_topology.py#L1648 In the line, ``None`` is passed to guess_water_box,...

prepare_dual_topology.py should generate position restraint files for the ligands and, when using system builder, for the receptor

3

According to some energy minimization and MD mdp files, positional restrains are desirable. However, the topology files do not have `[ position_restraints ]` in both complex and ligand systems. Also,...

Openeye license check

6

**Describe the bug** We have omega (but not omega toolkit) and oequacpac license. In this condition, openeye license check is not done correctly. **To Reproduce** ```python from openmm.app import PDBFile...