On Thu, Jun 15, 2017, Ashish Radadiya wrote:
>
> I tested mol2 file with "acdoctor" it also gave bunch of warnings.
Here's what I get with AmberTools17:
slater% antechamber -i isg.mol2 -fi mol2 -o dac.mol2 -fo mol2
Welcome to antechamber: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 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 --
/home/case/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (5) for atom (ID: 7, Name: C4).
Possible open valence.
Indeed, if you look at the bonds to atom 7:
10 6 7 ar
11 7 8 ar
12 7 10 2
You are asking for two aromatic bonds and one double bond to atom 7. This
adds up to 5 (1.5 + 1.5 + 2), just like the error message says.
I don't know how you got the mol2 file; for converting this to a pdb file
(which has no bond-order information), then using that as input to antechamber
worked fine for me.
....hope this helps....dac
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Received on Thu Jun 15 2017 - 13:00:03 PDT
