Hi George, What version of Chimera are you running? This problem: (DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib should be fixed in the 1.11 releases of Chimera. —Eric Eric Pettersen UCSF Computer Graphics Lab

On Aug 30, 2017, at 9:00 AM, George Tzotzos <gtzotzos@me.com> wrote:

I’ve loaded the prmtop and inpcrd of a protein in complex with a ligand (named DE3). I’ve tried to add ions to the complex using the Amber Tool.

I received the following message (see Reply log below). I wonder if I erred, in which case I would be grateful for any suggestions, or there’s a bug in the program.

Many thanks in advance

George

Assigning chain ID A to 125 residues, e.g. ASP Assigning chain ID B to 125 residues, e.g. ASP Model 0 (complex.inpcrd) appears to be a protein without secondary structure assignments. Automatically computing assignments using 'ksdssp' and parameter values: energy cutoff -0.5 minimum helix length 3 minimum strand length 3 Use command 'help ksdssp' for more information. /Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results in singular transformations; automatically expanding. left=1, right=1 + 'left=%s, right=%s') % (left, right)) Charge model: AMBER ff14SB Assigning partial charges to residue DE3 (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/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.in.mol2 -fi mol2 -o /var/folders/hd/94rkn65x0d75wdjf_5xmblp80000gn/T/tmpJfFWs_/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 (DE3)

(DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib

(DE3) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib

(DE3) Reason: image not found

(DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

(DE3)

(DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(DE3) Total number of electrons: 104; net charge: 0

(DE3)

(DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out

(DE3) 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 DE3 Check reply log for details _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users