[Chimera-users] chimera error during AddCharge for MD preparation

[Elaine Meng]

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 at 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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