[Chimera-users] Adding ions with Amber

Eric Pettersen pett at cgl.ucsf.edu
Wed Aug 30 10:35:12 PDT 2017

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 Pettersen
	UCSF Computer Graphics Lab

> On Aug 30, 2017, at 9:00 AM, George Tzotzos <gtzotzos at 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
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