<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Many thanks in advance</div><div class=""><br class=""></div><div class="">George</div><div class=""><br class=""></div><div class=""><div class="">Assigning chain ID A to 125 residues, e.g. ASP</div><div class="">Assigning chain ID B to 125 residues, e.g. ASP</div><div class="">Model 0 (complex.inpcrd) appears to be a protein without secondary structure assignments.</div><div class="">Automatically computing assignments using 'ksdssp' and parameter values:</div><div class=""> energy cutoff -0.5</div><div class=""> minimum helix length 3</div><div class=""> minimum strand length 3</div><div class="">Use command 'help ksdssp' for more information.</div><div class="">/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/matplotlib/axes.py:2369: UserWarning: Attempting to set identical left==right results</div><div class="">in singular transformations; automatically expanding.</div><div class="">left=1, right=1</div><div class=""> + 'left=%s, right=%s') % (left, right))</div><div class="">Charge model: AMBER ff14SB</div><div class="">Assigning partial charges to residue DE3 (net charge +0) with am1-bcc method</div><div class="">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</div><div class="">(DE3) </div><div class=""><br class=""></div><div class="">(DE3) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib</div><div class=""><br class=""></div><div class="">(DE3) Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib</div><div class=""><br class=""></div><div class="">(DE3) Reason: image not found</div><div class=""><br class=""></div><div class="">(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</div><div class=""><br class=""></div><div class="">(DE3) </div><div class=""><br class=""></div><div class="">(DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</div><div class=""><br class=""></div><div class="">(DE3) Total number of electrons: 104; net charge: 0</div><div class=""><br class=""></div><div class="">(DE3) </div><div class=""><br class=""></div><div class="">(DE3) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out</div><div class=""><br class=""></div><div class=""><u class=""><font color="#ff2600" class="">(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</font></u></div><div class=""><br class=""></div><div class="">Failure running ANTECHAMBER for residue DE3</div><div class="">Check reply log for details</div></div></body></html>