Re: [Chimera-users] Add Charges failure (libquadmath)

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 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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