Re: [AMBER] Odd number of electrons

From: Gustaf Olsson <>
Date: Wed, 24 Feb 2021 08:08:47 +0000

Looking at the PDB provided it is clear that the molecular charge is not zero.

There is a “carboxylate” group which, to produce a neutral structure, should be protonated (COOH and not COO-). Furthermore, there is a “nitro” group, while I am not sure regarding the importance of conservation of double bonds in PDB structure files, adding one for good measure might not be a bad idea.

Making these changes and performing a fast energy minimisation (not to convergence) successfully produced output using the antechamber input, as you supplied it.

If you need the deprotonated form of the acid, then the charge has to be set to -1 (nc -1).

Best regards
// Gustaf

> On 24 Feb 2021, at 05:43, divyabharathi korlepara <> wrote:
> 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"
> Thanks,
> Divya.
> Dr. Divya Bharathi,
> Post Doctoral Fellow,
> Hyderabad-500032.
> On Mon, Feb 22, 2021 at 11:50 PM David A Case <>
> wrote:
>> 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 Wed Feb 24 2021 - 00:30:02 PST
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