Hi,
1.
The problem with your first mol2 file is its first line which should
be two lines, not one:
===
.<TRIPOS>MOLECULE*****
===
Note that as Dave suggested this error is caught when acdoctor mode is on:
===
amber/bin/to_be_dispatched/antechamber: Fatal Error!
No ..<TRIPOS>MOLECULE field.
===
Note also that this error is caught by tleap:
===
> loadmol2 Oplus.mol2
Loading Mol2 file: ./Oplus.mol2
Error: Invalid MOL2 format.
Cannot find record type indicator: .<TRIPOS>MOLECULE
===
And if that error is fixed then antechamber performs as expected.
You could avoid that error by using redirection instead of cut-n-pasting:
$ obabel -:"[O+]" -o mol2 > Oplus.mol2
FWIW, antechamber is not robust with respect to file formats. It has
long been discussed to create a bullet proof library for file I/O...
2.
antechamber completely ignores record type UNITY_ATOM_ATTR and in the
next release will so announce:
===
Warning: Ignoring Mol2 record type (.<TRIPOS>UNITY_ATOM_ATTR).
===
scott
On Wed, Mar 31, 2021 at 08:45:28AM -0400, David A Case wrote:
> 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.
>
> ==========================================================================
> >
> >>$ 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.
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Received on Fri Apr 16 2021 - 19:30:03 PDT
