Re: [AMBER] Silica in antechamber

From: David A Case <>
Date: Tue, 19 Feb 2019 13:42:51 -0500

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.


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Received on Tue Feb 19 2019 - 11:00:03 PST
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