Dear Amber
I am trying to find to parameters for co-factor NADP+ by antechamber
But when I use this command:-
antechamber -i NADP_noH.mol2 -fi mol2 -o NADP_amber.mol2 -fo mol2 -c bcc
-pf yes -nc -3 -at gaff2 -j 4
It gives me this error
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 --
Warning: The number of bonds (1) for atom (ID: 33, Name: O1N) does not match
the connectivity (2) for atom type (O.3) defined in
CORR_NAME_TYPE.DAT.
Warning: The number of bonds (1) for atom (ID: 34, Name: O1X) does not match
the connectivity (2) for atom type (O.3) defined in
CORR_NAME_TYPE.DAT.
Warning: The number of bonds (1) for atom (ID: 39, Name: O2A) does not match
the connectivity (2) for atom type (O.3) defined in
CORR_NAME_TYPE.DAT.
Warning: The number of bonds (1) for atom (ID: 43, Name: O2X) does not match
the connectivity (2) for atom type (O.3) defined in
CORR_NAME_TYPE.DAT.
Warning: The number of bonds (3) for atom (ID: 55, Name: C4N) does not match
the connectivity (4) for atom type (C.3) defined in
CORR_NAME_TYPE.DAT.
Warning: The number of bonds (3) for atom (ID: 72, Name: N9A) does not match
the connectivity (2) for atom type (N.ar) 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/srania/Amber/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 55, Name: C4N).
Possible open valence.
Hoe to solve this issue
I have attached .mol2 file if there is something wrong please tell me.
thank you in advance
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Received on Sat Jun 22 2019 - 06:30:02 PDT
