On Fri, Feb 27, 2026, Priyasha Majee via AMBER wrote:
>
>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?
There is a real paucity of information here. Amber will never really form
extra bonds, and doesn't know anything about aromaticity. You may be
drawing conclusions about these aspects from a visualization program, which
have their own criteria.
If you are getting a "weird" structure for the ligand, it could well be due
to some misparameterization there. Looking close that what you think are
"extra bonds" might help focus your debugging efforts -- those are probably
close non-bonded contacts that should be investigated.
As a second suggestion, don't wait until after equilibration to look for
problems: look carefully at what happens at the very first (minimization)
steps. Use the cpptraj "checkstructure" action to look for problems in your
starting structure.
Beyond that, the mailing list needs more information to be of any help: we
don't know what G4 is, we don't know what the ligand is, we don't know what
you did to prepare the system, etc.
....good luck....dac
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Received on Fri Feb 27 2026 - 08:30:03 PST
