[Chimera-users] help with antechamber

Philip Hanley philiphanley at outlook.com
Sat Mar 12 07:49:06 PST 2016


To whom it concerns,
I’ve been using antechamber as part of a university project. I’m away from the university for the next few weeks and have downloaded chimera on my mac. I was using chimera on linux in the university. 
Im having the same issue, irregardless of what molecule i have, which is dock prep / add charge. I’m following the same procedure as i did in the university with molecules i know add charge did work for, but am receiving the following error;

Charge model: AMBER ff99SB
Assigning partial charges to residue TAG (net charge +0) with am1-bcc method
Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.in.mol2 -fi mol2 -o /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
(TAG) 

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

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

(TAG)   Reason: image not found

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

(TAG) 

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

(TAG) Total number of electrons: 98; net charge: 0

(TAG) 

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

(TAG) 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 TAG
Check reply log for details

Is there anything possible wrong with the general settings in the program that have to be changed? i have literally installed chimera, and changed no settings thus far. I have looked up forums relating to similar issues but have no found a solution.

Any help would be highly appreciated, 
thanks in advance, 
phil




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