one issue is that your prepi and frcmod don't have the same atom types
defined for the H atoms (H1 in prepi vs HC in frcmod).
On Tue, Feb 8, 2022 at 10:56 AM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> Please find parameters attached for methanol.
>
> Sincerely
> Debarati
>
>
> From: David A Case<mailto:david.case.rutgers.edu>
> Sent: Monday, February 7, 2022 9:45 PM
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] trouble finding vdW parameters for methanol
>
> On Mon, Feb 07, 2022, Debarati DasGupta wrote:
>
> >Loading parameters: ./frcmod.meoh
> >Loading Prep file: ./MOH.prepi
> >
> >1 of 9 atoms missing charges on atoms lines: methanol
> (This looks like a warning your should consider.)
>
> >Loading PDB file: ./MOH.pdb
>
> Where did these three files come from? Are you sure that that residue and
> atom names in MOH.pdb match exactly those in MOH.prepi? You may need to
> post the contents of these files.
>
> ....dac
>
>
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Received on Tue Feb 08 2022 - 08:30:02 PST
