Hi Rob,
"c3" is a type defined in GAFF (see file
amber/dat/leap/parm/gaff.dat,
for details). It is different from the type "C3" (note the case difference). Thus
the error message is correct.
To use GAFF atom types, you will have to add
source leaprc.gaff
to your leaprc.
However, I am not sure if you can use GAFF as a polarizable force field.
Sincerely,
Wei
On Apr 4, 2011, at 9:54 AM, r smith 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.
>
>
> Thanks,
>
> Rob
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Received on Mon Apr 04 2011 - 12:00:05 PDT
