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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Received on Mon Apr 04 2011 - 10:30:03 PDT
