[AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR

From: Alan <alanwilter.gmail.com>
Date: Wed, 31 Mar 2021 09:18:12 +0200

I'm wondering if this is a glitch or intended.

Using Open Babel 3.1.0 and Antechamber 20.0:

>$ obabel -:"[O+]" -o mol2
.<TRIPOS>MOLECULE*****
 1 0 0 0 0
SMALL
GASTEIGER

.<TRIPOS>ATOM
      1 O 0.0000 0.0000 0.0000 O.3 1 HOH1 1.0000
.<TRIPOS>UNITY_ATOM_ATTR
1 1
charge 1
.<TRIPOS>BOND
1 molecule converted

Putting that in file Oplus.mol2 and doing:

>$ antechamber -dr no -i Oplus.mol2 -fi mol2 -o tmp -fo ac -pf y


I got for tmp file:

CHARGE 4.00 ( 4 )
Formula: O4
ATOM 1 O HOH 1 0.000 0.000 0.000 1.000000 os
ATOM 2 O1 MOL 1 0.000 0.000 0.000 1.000000 os
ATOM 3 O2 MOL 1 0.000 0.000 0.000 1.000000 os
ATOM 4 O3 MOL 1 0.000 0.000 0.000 1.000000 os


Now, if I do (add option -xu to obabel):

>$ obabel -:"[O+]" -o mol2 -xu
.<TRIPOS>MOLECULE
*****
 1 0 0 0 0
SMALL
GASTEIGER

.<TRIPOS>ATOM
      1 O 0.0000 0.0000 0.0000 O.3 1 HOH1 1.0000
.<TRIPOS>BOND
1 molecule converted


I would get:

CHARGE 1.00 ( 1 )
Formula: O1
ATOM 1 O HOH 1 0.000 0.000 0.000 1.000000 os


Which is what I'd have expected in the first place.

Here's the doce about Mol2
http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf

I'm wondering how Antechamber is dealing with .<TRIPOS>UNITY_ATOM_ATTR
attribute. 
-- 
Alan Silva 🚲🏊‍♂🏃‍♂🇧🇷🇫🇷🇬🇧
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Received on Wed Mar 31 2021 - 00:30:02 PDT
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