Add Charges failure (libquadmath)
Hi There, I am trying to run charge calculation using Antechamber in chimera, but getting an error related to library not found. _______________________ Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.in.mol2 -fi mol2 -o /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (UNK) (UNK) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (UNK) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (UNK) Reason: image not found (UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (UNK) (UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (UNK) Total number of electrons: 302; net charge: 1 (UNK) (UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (UNK) 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 Failure running ANTECHAMBER for residue UNK Check reply log for details ----------------------- FYI, I am running on OS X EI Capitan version 10.11.5 Thanks, Subha
Hi Subha, This problem was fixed 11 months ago, so please update to a newer version of Chimera. Also, please report bugs by using the “Report A Bug” entry in Chimera’s Help menu rather than sending mail to the chimera-users list. Thanks! —Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 20, 2016, at 10:19 AM, Subha Kalyaanamoorthy <kalyaana@ualberta.ca> wrote:
Hi There,
I am trying to run charge calculation using Antechamber in chimera, but getting an error related to library not found. _______________________
Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.in.mol2 -fi mol2 -o /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (UNK)
(UNK) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib
(UNK) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib
(UNK) Reason: image not found
(UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC <http://antechamber_bond_type.ac/> -f ac
(UNK)
(UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC <http://antechamber_ac.ac/> -p gaff
(UNK) Total number of electrons: 302; net charge: 1
(UNK)
(UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in <http://sqm.in/> -o sqm.out
(UNK) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in <http://sqm.in/> -o sqm.out" of bcc() in charge.c properly, exit
Failure running ANTECHAMBER for residue UNK Check reply log for details -----------------------
FYI, I am running on OS X EI Capitan version 10.11.5
Thanks, Subha _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, Thanks very much for that info. You are correct, the latest version doesn't have this bug. Best Regards, Subha On Mon, Jun 20, 2016 at 1:12 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Subha, This problem was fixed 11 months ago, so please update to a newer version of Chimera. Also, please report bugs by using the “Report A Bug” entry in Chimera’s Help menu rather than sending mail to the chimera-users list. Thanks!
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 20, 2016, at 10:19 AM, Subha Kalyaanamoorthy <kalyaana@ualberta.ca> wrote:
Hi There,
I am trying to run charge calculation using Antechamber in chimera, but getting an error related to library not found. _______________________
Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.in.mol2 -fi mol2 -o /var/folders/pq/d4fvmdj542gcnqqjbfm554hr0000gt/T/tmpJCy8sw/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 (UNK)
(UNK) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib
(UNK) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib
(UNK) Reason: image not found
(UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC <http://antechamber_bond_type.ac/> -f ac
(UNK)
(UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC <http://antechamber_ac.ac/> -p gaff
(UNK) Total number of electrons: 302; net charge: 1
(UNK)
(UNK) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out
(UNK) 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
Failure running ANTECHAMBER for residue UNK Check reply log for details -----------------------
FYI, I am running on OS X EI Capitan version 10.11.5
Thanks, Subha _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Dr. Subha Kalyaanamoorthy Post Doctoral Fellow Faculty of Pharmacy and Pharmaceutical Sciences University of Alberta Edmonton, Canada.
participants (2)
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Eric Pettersen -
Subha Kalyaanamoorthy