Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom

From: David A Case <>
Date: Fri, 8 Jan 2021 10:01:31 -0500

On Wed, Jan 06, 2021, Mateusz Bieniek wrote:
>I could use a bit of help with a strange situation with the .mol2 format.
>There is an empty line in my .mol2 file just before the ".<TRIPOS>BOND"
>section. This is a file generated by another package.
>It seems to me that the mol2 format defined Blank Line which is ignored by
>the MOL2 command (,
>page 3).
>However, to my surprise, when I use antechamber
>antechamber -i test.mol2 -fi mol2 -o out.mol2 -fo mol2 -dr no
>It generates an extra atom in my file in the ATOM section.

Thanks for your report. I'm cc-ing to Scott and Junmei, who are probably in
the best position to make sure that antechamber is ignoring blank lines in
mol2 files.


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Received on Fri Jan 08 2021 - 07:30:02 PST
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