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

From: Mateusz Bieniek <bieniekmat.gmail.com>
Date: Wed, 6 Jan 2021 14:40:28 +0000

Hi there,

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 (http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf,
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. Whereas the
command appears mineangless, it is a part of the pipeline and serves its
purpose. Regardless, I would not expect antechamber to generate an atom
just because there is a blank line in the .mol2 file.

I attach the test.mol2 file and the output out.mol2 file.


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Received on Wed Jan 06 2021 - 07:00:02 PST
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