Yes I have lots of atom in a silica lattice. Right, Thank you for your
answer
On Tue, Feb 19, 2019 at 1:43 PM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Feb 19, 2019, Hadi Rahmaninejad wrote:
> >
> >As we know we amber forcefield is not supporting inorganic elements like
> >silica lattice. I obtained mol2 file and trying to get "prepi" file from
> >antechamber with this command:
> >" antechamber -i silica.mol2 -fi mol2 -o silca.prepi -fo prepi", but I got
> >this error message:
> >
> >"Info: The number of bonds (512) exceeded MAXBOND.
> >
> >---Judge bond type for Residue 1 with ID of 1 and Name of XXX ---
> >
> >---Judge bond type for Residue 2 with ID of 2 and Name of XXX ---
> >
> >---Judge bond type for Residue 3 with ID of 3 and Name of XXX ---
>
> Can you provide your input mol2 file? It looks like it has several
> residues, and (perhaps) lots of atoms. Remember that antechamber is
> intended for *small* (drug-like) molecules. If you are trying to use if
> for a silicon lattice, you are way outside its intended area of use.
>
> ...dac
>
>
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Received on Tue Feb 19 2019 - 11:30:03 PST
