Hi
Did you image all the frames to the central box before visualizing?
“autoimage” command in cpptraj should be sufficient.
Computing rmsd should indicate if the system is moving too much.
On Friday, 27 February 2026, Priyasha Majee via AMBER <amber.ambermd.org>
wrote:
>
>
> 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
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best Regards
Elvis
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Received on Thu Feb 26 2026 - 23:00:04 PST
