Re: [AMBER] Odd number of electrons

From: divyabharathi korlepara <>
Date: Wed, 24 Feb 2021 10:13:25 +0530

Dear DAC,
           I have tried with the PDB file as input still it is giving me
the error. The charge of the system is 0.
antechamber -fi pdb -fo mol2 -i ligand.pdb -o ligand_clean_h.mol2 -rn LIG
-c bcc -pf y -at gaff2 -nc 0 -ek "maxcyc=0, ndiis_attempts=700"

Dr. Divya Bharathi,
Post Doctoral Fellow,

On Mon, Feb 22, 2021 at 11:50 PM David A Case <>

> 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
> >-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
> _______________________________________________
> AMBER mailing list

AMBER mailing list

Received on Tue Feb 23 2021 - 21:00:02 PST
Custom Search