On Wed, Mar 31, 2021, Alan wrote:
>I'm wondering if this is a glitch or intended.
>
>Using Open Babel 3.1.0 and Antechamber 20.0:
The design goal of antechamber is to determine Amber or GAFF atom types by
examining the actual geometry that is entered, pretty much ignoring any atom
types that might be in an input mol2 file. (This is why, for example, it
requires hydrogens to be present.) It was never designed to be a
general-purpose mol2 file interpreter.
So, giving antechamber a "molecule" consisting of a single charged oxygen
atom is likely to lead it astray. Leaving out the "-dr no" flag may help in
deciphering what it is trying to do.
It does sound like antehcamber might be improperly parsing a UNITY_ATOM_ATTR
record. I'll cc- this to Junmei Wang, who may wish to look at this. But
the safest thing to do is to feed antechamber a PDB-format file.
...hope this helps....dac
==========================================================================
>
>>$ 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
>https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fchemyang.ccnu.edu.cn%2Fccb%2Fserver%2FAIMMS%2Fmol2.pdf&data=04%7C01%7Cdavid.case%40rutgers.edu%7Cf7838f82fc894b6a9e5d08d8f41549ca%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C637527719565331758%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=UNXiXB8uAtE%2BmML8IpGe55mgX26%2BAh6IG2G37Kqx798%3D&reserved=0
>
>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 - 06:00:04 PDT
