I'm trying to model a zinc binding protein, where the zinc is coordinated by two cysteines, a histidine and a glutamic acid. The bonds are present in the CONECT records of the template. I added upper bound restraints to restrain all distances between the zinc and the four coordinating atoms, and used
"rsr.excluded_pairs.append" to exclude the bonds between the zinc and the four coordinating atoms from the nonbonded list. Models were built via the loopmodel routine. In the resulting models, the sulfur atoms are moving away from the zinc, as if the cysteine sulfurs are protonated.
What is the best way to prevent this? Is there an easy way to define the cysteines as unprotoneated?