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 - 16:30:02 PDT
