On Sat, May 16, 2020, Lod King wrote:
>Sorry that I did not attach the file, here it is the furazan molecule in
>mol2.
I can't reproduce any problem here, with this antechamber run:
antechamber -fi mol2 -i furazan.mol2 -fo mol2 -o foo.mol2
Here is output:
----------------------------------------------------------------------------
Welcome to antechamber 20.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
-- Check Format for mol2 File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: The number of bonds (3) for atom (ID: 2, Name: N) does not match
the connectivity (4) for atom type (N.4) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (3) for atom (ID: 3, Name: N1) does not match
the connectivity (4) for atom type (N.4) 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 --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
----------------------------------------------------------------------------
I've attached the output mol2 file (with gaff atom types).
So: what version of AmberTools are you using? Are you doing what I
outlined above? It seems possible that having the N atoms identified as
N.4 could cause a problem, but I'm not seeing it.
If you can't get things to work, we will need *full* details of exactly
what was done, in order to try to reproduce the behavior you see.
....dac
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Received on Tue May 19 2020 - 05:30:03 PDT
