[Chimera-users] Add Charges failure (libquadmath)

[Eric Pettersen]

Hi Lluis,
	Thanks for reporting the problem.  After some detective work, we’ve discovered that it is only a problem in the 32-bit version of the daily build.  We will try to have a fix in for tomorrow’s daily build but in the meantime if you use the 64-bit version then things will work.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 25, 2016, at 9:00 AM, Lluis Blancafort <lluis.blancafort at udg.edu> wrote:
> 
> Hi,
> 
> 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?
> 
> Thanks!
> 
> Lluís Blancafort
> Institut de Química Computacional i Catàlisi
> Universitat de Girona
> 17071 Girona
> Spain
> 
> (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) 
> 
> (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) 
> 
> (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) 
> 
> (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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