Dear Amber Users,
I optimised a ligand using gaussian and after normal termination tried to parametrize the same using antechamber, on which I received the following warning at the initial step.
Warning: ATOM N3 has unfilled valence, assuming the linked atom name (in other residue) is "M"
change "M" to "-M" if ATOM N3 is linked to the immediate previous residue
change "M" to "+M" if ATOM N3 is linked to the immediate after residue
However, proceeding further the error appeared which says,
***********************************************************
Welcome to antechamber 21.0: molecular input file processor.
acdoctor mode is on: check and diagnose problems in the input file.
The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for mol2 File --
Status: pass
Warning: Unknown bond type for bond (C1-C6:Ar).
Assuming it is a single bond.
Warning: Unknown bond type for bond (C2-C3:Ar).
Assuming it is a single bond.
Warning: Unknown bond type for bond (C3-C4:Ar).
Assuming it is a single bond.
Warning: Unknown bond type for bond (C4-C5:Ar).
Assuming it is a single bond.
Warning: Unknown bond type for bond (C4-N21:Ar).
Assuming it is a single bond.
Warning: Unknown bond type for bond (C8-N22:Ar).
Assuming it is a single bond.
Warning: Unknown bond type for bond (C9-N23:Ar).
Assuming it is a single bond.
Warning: Unknown bond type for bond (C10-N24:Ar).
Assuming it is a single bond.
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Warning: The number of bonds (4) for atom (ID: 13, Name: C13) does not match
the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 17, Name: C17) does not match
the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 21, Name: N21) does not match
the connectivity (3) for atom type (N) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 23, Name: N23) does not match
the connectivity (3) for atom type (N) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 28, Name: C28) does not match
the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 31, Name: C31) does not match
the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 33, Name: C33) does not match
the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 35, Name: C35) does not match
the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (4) for atom (ID: 37, Name: C37) does not match
the connectivity (3) for atom type (C) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 40, Name: O40) does not match
the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 42, Name: O42) does not match
the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 44, Name: O44) does not match
the connectivity (1) for atom type (O) defined in CORR_NAME_TYPE.DAT.
Warning: The number of bonds (2) for atom (ID: 46, Name: O46) does not match
the connectivity (1) for atom type (O) 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/xxxxx/AMBER/amber20/bin/wrapped_progs/antechamber: Fatal Error!
Weird atomic valence (3) for atom (ID: 3, Name: C3).
Possible open valence.
********************************************************************
I did try looking for this warning in the AMBER mailing list archives and also found one similar, but could not understand the solution.
Can you please help solving this open valence error.
Thank you and regards.
Madhusmita Devi
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Received on Thu Jan 12 2023 - 00:00:03 PST
