you need to edit the file as DAC suggested, where your prepi, frcmod and
pdb all agree on atom names and atom types.
On Tue, Feb 8, 2022 at 11:48 AM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> http://amber.manchester.ac.uk/
>
> This is the database where I got the parameters from.
> Anyway I can remediate this?
> Thanks
> Debarati
>
>
>
>
>
> From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
> Sent: Tuesday, February 8, 2022 11:04 AM
> To: AMBER Mailing List<mailto:amber.ambermd.org>
> Subject: Re: [AMBER] trouble finding vdW parameters for methanol
>
> 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 - 09:00:03 PST
