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