[AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer

From: Lod King <lodking407.gmail.com>
Date: Fri, 15 May 2020 08:36:08 -0700

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

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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Received on Fri May 15 2020 - 09:00:02 PDT
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