Hi Sorin,
I followed tutorial on amber website:
https://ambermd.org/tutorials/advanced/tutorial35/index.php
I also wrote python script (see attached) that reads topology without
lone pairs and generates rules file used as input to mdgx.
Juraj
On 27. 08. 24 11:21, Sorin Draga via AMBER wrote:
> 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 - 03:00:02 PDT
