chimera error during AddCharge for MD preparation
Hi, I am attempting to perform MD stimulations with a protein containing an FAD cofactor, however, I keep receiving the following error message: Charge model: AMBER ff14SB Assigning partial charges to residue FAD (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.in.mol2 -fi mol2 -o /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 (FAD) (FAD) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib (FAD) Referenced from: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib (FAD) Reason: image not found (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (FAD) Total number of electrons: 408; net charge: -2 (FAD) (FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out (FAD) Error: cannot run "/Users/alwaterbury/Desktop/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 FAD Check reply log for details Any help/suggestions would be much appreciate! Best, Amanda
Hi Amanda, You could try using the other, simpler charge-calculation method (Gasteiger), for FAD. The am1-bcc method tends to have a hard time with large and/or highly charged species like nucleotides. We have lookup tables for ATP and several others, but unfortunately not FAD currently. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html#antechamber> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 4, 2018, at 7:12 AM, Waterbury, Amanda <alwaterbury@g.harvard.edu> wrote:
Hi, I am attempting to perform MD stimulations with a protein containing an FAD cofactor, however, I keep receiving the following error message:
Charge model: AMBER ff14SB Assigning partial charges to residue FAD (net charge -2) with am1-bcc method Running ANTECHAMBER command: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.in.mol2 -fi mol2 -o /var/folders/wd/pdz6gvr12ybbxtfs6m6mn1y80000gn/T/tmpUR9bIs/ante.out.mol2 -fo mol2 -c bcc -nc -2 -j 5 -s 2 (FAD)
(FAD) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib
(FAD) Referenced from: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib
(FAD) Reason: image not found
(FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
(FAD)
(FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
(FAD) Total number of electrons: 408; net charge: -2
(FAD)
(FAD) Running: /Users/alwaterbury/Desktop/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out
(FAD) Error: cannot run "/Users/alwaterbury/Desktop/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 FAD Check reply log for details
Any help/suggestions would be much appreciate! Best, Amanda
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Elaine Meng -
Waterbury, Amanda