Thanks for the reply. You are correct
On Mon, Apr 4, 2011 at 1:15 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Apr 4, 2011 at 7:54 AM, r smith <rsl04f.gmail.com> wrote:
>
> > Hello,
> >
> > After producing my .mol2 file with antechamber, I am using sleap to
> prepare
> > inputs for the ff02pol.r1 force field.
> >
> > However, I receive an error after the following commands:
> >
> > [gtkleap]$ source leaprc.ff02pol.r1
> > [gtkleap]$ mol = loadmol2 em_ac.mol2
> > [gtkleap]$ saveAmberParmPol mol prmtop inpcrd
> > Error: unknown atom type: c3
> >
> > It is not clear why the atom type is unrecognized since C3 appears to be
> in
> > the leaprc.ff02pol.r1 file. Does anyone know why this error would occur?
> > The mol2 file is attached.
> >
>
> c3 is not C3. It looks like you used antechamber to create this mol2. If
> that's the case, make sure that you use AMBER atom types and not gaff (it
> appears that you used gaff here). I'm only reporting here why you're
> getting the error you're getting, as I have no experience using polarized
> force fields. I'm not sure what the proper way of parametrizing a new
> ligand for ff02pol is.
>
> Hope this helps,
> Jason
>
>
> >
> >
> > Thanks,
> >
> > Rob
> >
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> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
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Received on Mon Apr 04 2011 - 12:00:06 PDT
