Carlos

write_traj problem when selecting a mask and specific frames

1

Hi, I'm trying to save multiple frames from a trajectory, extracting only a selection (with mask) of atoms/residues `pt.write_traj('t.pdb',traj,overwrite=True,options='multi',frame_indices=range(0,traj.n_frames,int(traj.n_frames/int(frames))))` This creates a single pdb file without problems. But when trying...

TypeError: no default __reduce__ due to non-trivial __cinit__ pmap/watershell

6

Hi, Some info: I installed ambertools via conda as explained here: https://ambermd.org/GetAmber.php Everything went well, without problems. But when trying to run wathershell: shell_anions = pt.pmap(pt.watershell, traj, solute_mask=' :1', solvent_mask=':Cl-',...

Unstable simulation

4

Hi, I'm trying to parametrize a small molecule. I was able to create both, the .itp and .gro files without issues. After this I first minimize in vaccum the molecule...

- [ ] I believe this to be a bug with LigParGen - [ ] This is a feature request ## Issue Information Software name & Version :LigParGen Method:LigParGen ##...