Hi,
Try running parmchk on your ligand, e.g.
parmchk -i caryo.mol2 -fi mol2 -o caryo.frcmod
This will generate a frcmod file with the missing parameters. You
should visually inspect these parameters to make sure they look
reasonable. See sections "4.1.2 parmchk" and "4.2 A simple example for
antechamber" in the AmberTools user manual for further examples.
-Dan
On Fri, Apr 8, 2011 at 5:07 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I'm trying to generate ligand input files for an MD ligand/protein simulation.
>
> My ligand is caryophyllene (see snapshot)
>
> The ligand caryo.pdb has been generated with Chimera and the caryo.mol2 file with antechamber.
>
> Checking the unit ("check CARYO) gives the following output
>
>
> Checking 'CARYO'....
> Checking parameters for unit 'CARYO'.
> Checking for bond parameters.
> Checking for angle parameters.
> Could not find angle parameter: cy - c2 - c3
> Could not find angle parameter: c2 - cy - hc
> There are missing parameters.
> Unit is OK.
>
> I'm reluctant to continue given that the above parameters are missing.
>
> I'd appreciate any suggestion on solving this problem
>
> A good evening to all
>
> George
>
>
>
>
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Received on Fri Apr 08 2011 - 14:30:06 PDT
