Hi,
Frankly speaking, I just want to use the mol2 file to generate prepc and
frcmod files for my ligand. I don't extract RES from the mol2 files.
For sure, my bond order for the oxygen is wrong.
This molecule is having a furazan scaffold: one oxygen is bonded with two
nitrogens, and I tested the furazan molecule, it did give me the same
error.
So I don't know why even furazan would lead to such error. I was
anticipating that my ligand would since it is not a regular molecule.
On Fri, May 15, 2020 at 4:02 PM Renato Araujo <renatoacufpa.gmail.com>
wrote:
> Hi
>
> This indicates a problem with your molecule
>
> You should check if there are no extra bonds in this atom that is causing
> problems.
>
> Are you trying to extract RES loads from the binder?
> if the answer is yes, try the commands below.
>
> antechamber -fi gout -fo ac -nc 0 -i lig.log -o lig_resp.mol2 -c resp
> parmchk2 -i lig_resp.mol2 -f mol2 -o lig_resp.frcmod
>
> See if it works
>
> Att.,
>
> Dr Renato Costa
>
> Em sex., 15 de mai. de 2020 às 12:36, Lod King <lodking407.gmail.com>
> escreveu:
>
> > Hi Amber
> >
> > I got the following error when using $antechamber to generate prepc and
> > frcmod files
> >
> > ~~~~~
> >
> > Welcome to antechamber 17.3: molecular input file processor.
> >
> >
> > acdoctor mode is on: check and diagnosis problems in the input file.
> >
> > -- Check Format for mol2 File --
> >
> > Status: pass
> >
> > Info: Finished reading file (st0.mol2).
> >
> > -- Check Unusual Elements --
> >
> > Status: pass
> >
> > -- Check Open Valences --
> >
> > Warning: The number of bonds (2) for atom (ID: 7, Name: O) does not match
> >
> > the connectivity (1) for atom type (O.2) defined in
> > CORR_NAME_TYPE.DAT.
> >
> > But, you may safely ignore the warnings if your molecule
> >
> > uses atom names or element names as atom types.
> >
> > -- Check Geometry --
> >
> > for those bonded
> >
> > for those not bonded
> >
> > Status: pass
> >
> > -- Check Weird Bonds --
> >
> > /home/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> >
> > Weird atomic valence (3) for atom (ID: 7, Name: O).
> > Please check atomic connectivity.
> > ~~~~~~~~~
> >
> > how should I fix it? my O is connected by two Ns in a five-member ring,
> > btw.
> >
> > Thanks for your help!
> > _______________________________________________
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> >
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Received on Fri May 15 2020 - 21:30:02 PDT
