Hi Amber community,
I get a weird error with antechamber. I believe this is a mac problem but wondering if anyone knows a way around it.
When i conduct
% antechamber -fi pdb -fo mol2 -i MNS_fixed_H.pdb -o MNS_pre.mol2 -c bcc -pf y -nc -1
Welcome to antechamber 22.0: molecular input file processor.
Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
-- Check Format for pdb 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 --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Info: Bond types are assigned for valence state (2) with penalty (1).
Info: Total number of electrons: 132; net charge: -1
Running: /opt/anaconda3/envs/AmberTools2023/bin/sqm -O -i sqm.in -o sqm.out
*
No issues arises.
When i run
antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o cro.ac -c bcc -at amber
Welcome to antechamber 22.0: molecular input file processor.
Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to amber; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
/opt/anaconda3/envs/AmberTools2023/bin/wrapped_progs/antechamber: Non Fatal Error!
Residue (CRO) has a type of LINKING.
This linking monomer will likely become part of a polymer
and thus probably requires special handling beyond antechamber.
Ignore this error only if you know what you are doing.
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- 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.
/opt/anaconda3/envs/AmberTools2023/bin/antechamber: line 9: 9378 Illegal instruction: 4 "$AMBERHOME/bin/wrapped_progs/antechamber" "$@"
I tried in bash, csh and zsh just in case, i can see that bin/antechamber has a line with $@ but i dont know whats wrong with this command
Any advice would be appreciated
Kind regards,
Ingso
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Received on Sun Jun 23 2024 - 20:00:02 PDT
