Ricardo Ramirez
Ricardo Ramirez
It does not read my gro file and my trajectory despite the fact that I deleted water to make it faster. It freezes at collect from trajectories
The current MDAnalysis atom guesser incorrectly assigns the element type for certain atoms. This misassignment leads to incorrect bond guessing, particularly in DSM lipids—which is how the issue was originally...
Expected Behavior When using guess_TopologyAttrs to generate bonds for DSM lipids, the bonds around atom C3S (or any C*S) should be guessed correctly. For example: ("C3S", "C4S"), ("C3S", "C2S"), ("C3S",...