madh amicyanin outputs (psf, pdb) from namd setup for a single point energy calc
vmd successfully creates pdb and psf files but there are some parameter names that need to be fixed to run the namd minimization
ignore namd generated files
rearanged via ruby script residue order in proteinB.pdb to generate ttq with the correct coordinates
all bonds are created correctly for ttq. solvate box
oxidized minimization working
template for running qm/mm single point energy calculation
Merge branch 'madham_oxidized_patch'