Re: [AMBER] Antechamber Charge Methods

From: Sofia Vasilakaki <>
Date: Tue, 2 Jul 2019 00:08:02 +0300

If -c rc not used, then mol2 file returns with no charges.

-cf : not sure how it works.

I am using a text editor to edit mol2 but it would be rather convenient if
I could do it in the command line. I have more than 10 molecules to

Thank you,

> On Mon, Jul 01, 2019, Sofia Vasilakaki wrote:
>>I would like to use the charges included in the Jaguar Output (for a
>> small
>>organic molecule) in Antechamber to generated the mol2 file. How I could
>>do this?
>>I have tried
>>antechamber -i jag_name.out -fi jout -o name.mol2 -fo mol2 -c rc
>>but it generates an error: Cannot open file () with mode (r)
> What happens if you leave out the "-c rc" part? You could also play
> around with the "-cf" flag, but then I don't understand how the code
> knows that the charge file is a Jaguar output file.
> cc-ing to Junmei Wang, who is the author.
> The "simple" thing is to just use a text editor to edit the mol2 file
> and enter the charges by hand from the jaguar output.
> ...good luck...dac
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Received on Mon Jul 01 2019 - 14:30:02 PDT
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