Veronica,
although I'm no expert in RNA simulations, I'm not sure whether your
parameterization ansatz was successfull: Parameterization approaches
normally comprise only that units of a systems, for which no parameters
are available; but a ligand charge of -684 suggests that your "unit" is
much too large.
Maybe you could cut your system in smaller pieces, re-use existing force
field parameters for known units and parameterize only unknown units.
Thus, the problem may not be the charge difference between your ligands
but the parameterization ansatz (with the resulting parameters and
atomic charges).
Since you provided no further details about your system, your
parameterization, and your simulation, it's hard give additional pieces
of advice (perhaps I misunderstood your question?), but maybe some
experts can chime in here.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 29.09.2023 um 10:18 schrieb VERONICA MARTIN HERNANDEZ via AMBER:
> Hi everyone
>
> I've trying the parametrization of a ribosoma-ligand complex. It works well with some ligands but other ligands can't be minimized without "exploiding". The difference between the ligands that work and the ligands that don't is that the first have a -683.99 charge and the second have -684.005. I want to perform all the MD with the same parameters in order to compare the results but I don't know how to fix it.
> What should I do?
> Thanks in advance
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Received on Fri Sep 29 2023 - 03:00:02 PDT
