[Chimera-users] Add Charges failure (libquadmath)

Lluis Blancafort lluis.blancafort at udg.edu
Mon Jan 25 09:00:10 PST 2016


I’m running Chimera alpha version 1.11 on Mac OSX El Capitan 10.11.2

The Add Charges tool does not work for non-standard residues with AM1-BCC. The Reply Log reports a problem with libquadmath and later with sqm utility (see below). I don’t have libquadmath.0.dylib installed.

Can anybody help?


Lluís Blancafort
Institut de Química Computacional i Catàlisi
Universitat de Girona
17071 Girona

(1) Charge model: AMBER ff14SB
Assigning partial charges to residue SGA (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.in.mol2 -fi mol2 -o /var/folders/6j/nf071g8n2b5csd0rdcm8n5sc0000gn/T/tmpKi57P0/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2

(SGA) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib

(SGA)   Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib

(SGA)   Reason: image not found

SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac


(SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(SGA) Total number of electrons: 136; net charge: -1


(SGA) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out

(SGA) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit

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