Thank you both for all these informative updates.
On Sat, 17 Apr 2021 at 04:04, Scott Brozell <sbrozell.comcast.net> wrote:
> 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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--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
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Received on Mon Apr 19 2021 - 04:00:02 PDT
