Hi all,
I am trying to simulate G4 and the ligand complex. But I am facing some
problems. After the equilibration stage, my ligand is distorting,
forming unwanted extra bonds, aromatic rings losing their aromaticity.
When preparing the structure in tleap, no errors are showing up. But
when visualized after equilibration, the molecule is turning into weird
structure. Can someone help me fix this?
Regards,
Priyasha Majee
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 26 2026 - 23:00:02 PST
