The reason this is happening is probably because the atom type in your input .ac file has a different bond order than that of Amber’s database.
The atom type may have changed accidentally when you converted file type (from pdb to mol2).
Did you start with a mol2?
A quick fix is to make sure the atom type in your input .ac file for that C1 carbon is correct-assuming of course the connectivity is correct.
Sent from my iPhone
> On Sep 26, 2019, at 1:27 AM, Renato Araujo <renatoacufpa.gmail.com> wrote:
>
> dear colleagues and friends
>
> Someone, please help me resolve this error:
>
> I am using the following command
>
> antechamber -fi ac -i input.ac -c wc -cf input.crg
>
> And this happening:
>
> Welcome to antechamber 17.3: molecular input file processor.
>
> acdoctor mode is on: check and diagnosis problems in the input file.
> - Check Format for ac File -
> Status: pass
> - Check Unusual Elements -
> Status: pass
> - Check Open Valences -
> Status: pass
> - Check Geometry -
> for those bonded
> for those not bonded
> Status: pass
> - Check Weird Bonds -
> / usr / local / Chem / amber18 / bin / to_be_dispatched / antechamber:
> Fatal Error!
> Weird atomic valence (1) for atom (ID: 1, Name: C1).
> Possible open valence.
>
> How to solve ?
>
> Thanks
>
> Dr Renato Costa
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Received on Wed Sep 25 2019 - 19:30:02 PDT
