Have you tried it in Amber? This may be a Desmond issue.
Also, ff19sb may not be supported in Desmond.
Finally, thr message suggests you may be using tip3p. This is not a good
combination, see the ff19sb paper for details. You want a better water
model.
On Fri, Dec 6, 2024, 10:22 AM Zeyu Lin via AMBER <amber.ambermd.org> wrote:
> Hello amber users,
>
> I used *Antechamber* to create a ligand template for my cyclic peptide
> ligand and converted it to a format suitable for Desmond using
> *viparr-convert-amber*. I then processed my protein-ligand complex using
> this template along with *amber19sb*. However, I keep encountering the
> following error:
>
> schrodinger.infra.structure.PyStructureReaderException: Could not extract
> mmct handle (File: desmond_setup_AgrC_AIPI_TIP3P-out_viparr.cms):
> FATAL: * MCT FATAL(-5): mmct_ct_mi2io_get_atom():
> CT 0: Error getting data for atom: '1'
>
> Does anyone know how to solve this?
>
> Many thanks,
> Zeyu
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>
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Received on Sat Dec 07 2024 - 07:00:02 PST
