Re: [AMBER] Odd number of electrons

From: David A Case <>
Date: Mon, 22 Feb 2021 13:19:50 -0500

On Mon, Feb 22, 2021, divyabharathi korlepara wrote:

> I am using antechamber to generate GAFF parameters for a ligand
>molecule. I have used the following command to do that.
>antechamber -fi mol2 -fo mol2 -i ligand.mol2 -o ligand_clean_h.mol2 -rn LIG
>-c bcc -pf y -at gaff2 -ek "maxcyc=0, ndiis_attempts=700"

Try converting your input structure to PDB format, and using that as the
input to antechamber. Antechamber will figure out the connectivity from
the structure.

If you still have problems, please post the pdb file rather than a
screenshot. It's hard to see where atom #31 is from your figure.

You subject of your email was "odd number of electrons", but there was
nothing about this in the body of the email. If you ligand is charged, you
will need to use the "-nc" flag in antehchamber to tell it that.

...good luck...dac

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Received on Mon Feb 22 2021 - 10:30:03 PST
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