[Chimera-users] Adding ions with Amber

George Tzotzos gtzotzos at me.com
Wed Aug 30 09:00:06 PDT 2017

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


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) 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) 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) 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
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