Dear AMBER community,
I am currently preparing a large system (ion channel) with a halogenated
ligand, using CHARMM-GUI and the associated CGENFF service for ligand
parametrization.
However, in the past, MD simulations failed because of the presence of the
LP1 (lone pair) pseudoatom (as far as I remember lone pairs were not
supported in AMBER ffs but I might be wrong).
Has this changed in the new AMBER version?
What would be some alternative solutions to the problem? I seem to recall a
suggestion on the mailing list for simply removing these LPs, but I cannot
find it at the moment.
Many thanks as always for the excellent advice 🙂
Kind regards,
Sorin
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Received on Tue Aug 27 2024 - 02:30:02 PDT
