id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4251	Add Charge trying to use local libquadmath	Elaine Meng	Eric Pettersen	"I can use Chimera addcharge on 1xf6, which has inline MEN (methylasparagine) and LYZ (hydroxylysine), after deleting solvent, ions, and ligands for convenience. However, in ChimeraX, ""coulombic"" charge calculation dies on the MEN residue, doesn't get to the LYZ:

coulombicUsing Amber 20 recommended default charges and atom types for standard residues
Assigning partial charges to residue MEN (net charge +0) with am1-bcc method
Running ANTECHAMBER command: /Users/meng/Desktop/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/5y/hlccmqph8xj29d001s70mt7r0000gr/T/tmppk6jjdhi/ante.in.mol2 -fi mol2 -o /var/folders/5y/hlccmqph8xj29d001s70mt7r0000gr/T/tmppk6jjdhi/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(MEN)
(MEN) Welcome to antechamber 20.0: molecular input file processor.
(MEN)
(MEN) Info: Finished reading file (/var/folders/5y/hlccmqph8xj29d001s70mt7r0000gr/T/tmppk6jjdhi/ante.in.mol2); atoms read (29), bonds read (28).
(MEN) Info: Determining atomic numbers from atomic symbols which are case sensitive.
(MEN) Running: /Users/meng/Desktop/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(MEN)
(MEN)
(MEN) Running: /Users/meng/Desktop/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(MEN) Info: Total number of electrons: 108; net charge: 0
(MEN)
(MEN) Running: /Users/meng/Desktop/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out
(MEN) dyld: Library not loaded: /usr/local/gfortran/lib/libquadmath.0.dylib
(MEN) Referenced from: /Users/meng/Desktop/ChimeraX_Daily.app/Contents/lib/libgfortran.3.dylib
(MEN) Reason: image not found
(MEN) /Users/meng/Desktop/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber: Fatal Error!
(MEN) Cannot properly run ""/Users/meng/Desktop/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".

Tested in UCSF ChimeraX version: 1.2.dev202102121952 (2021-02-12) on mac.

Another structure 6khh containing LYZ but not MEN turned out to be a bad test because in both Chimera and ChimeraX, hydrogens are added incorrectly to that LYZ (treated as C=O carbonyl instead of sp3 CHOH) probably because it doesn't have very good bond lengths.
"	defect	closed	moderate		Structure Editing		fixed						all	ChimeraX