Building the GFP input file

Download the crystal structure 1W7S - http://www.pdb.org/pdb/explore/explore.do?structureId=1W7S Media:1W7S.pdb
Open the file in Gaussview 5 without water, add hydrogens if none present (dont drag file ont Gaussview, open and change opening options)
In the PDB secondary structure editor, delete chains B,C and D Media:1W7S_Chain_A.gjf
Clean up chromophore - delete hydrogens placed incorrectly on the chromophore Media:1W7S_Chain_A_cleaned.gjf
Open the PDB residue editor and protonate/deprotonate each residue in line with your selected pH environment Media:1W7S_cleaned_pH_7.gjf
Since the chromophore contains centers which are undefined in the AMBER force field to avoid errors, add wildcard parameters set to 0 in the input file and freeze the involved centers in the group editor, add the "hardfirst" keyword to read the additional parameters Media:1W7S_cleaned_wildcards_frozen.gjf
The previous input has NO charges, to add charges first need to find the full overall charge, in the atom editor add AMBER94 charges to ALL atoms and run an energy calculation, the output file will list the charge breakdown over residues and an overall charge. From this it is easy to tell the overall charge is -6. Media:1W7S_cleaned_energy_AMBER_charges.log
Now specify the overall charge as -6, delete all charges in the atom editor, run an energy calculation with the qeq keyword to retrieve partial charges across the entire molecule. INPUT:Media:1W7S_-6_qeq_charges.gjf OUTPUT: Media:1W7S_-6_qeq_charges.log
The fchk will contain the Qeq Charges, in the log file you can see that all atoms now have assigned charges. There is also a warning that some atoms now have charges but no Van der Waals parameters, this means that they can collapse onto other centers in an optimisation causing the job to fail. These charges were set to 0 to get an optimisation to run, they all corresponded to alcohol protons. Since the fchk must be used to carry the charges through to the next calculation you lose all residue information but this can be pasted back into the input file since all connectivity is the same. INPUT: Media:1W7S_qeq_opt_ready.gjf OUTPUT: Media:1W7S_qeq_opt_ready.log‎
This input has the correct protonation state for pH7, Qeq generated charges totaling the overall charge, and runs a successful geometry optimisation (although frozen chromophore means its not a minimum). I have not pasted the residue information back in but this is simple.
The process to paste back protein information is not trivial! The final file includes the correct protonation state for pH7, Qeq generated charges totaling the overall charge (-6) and all avaliable PDB information (residue and secondary structure information) [[Media:‎]]

It is noted that since the charges which were on 0 Van der Waals atoms were deleted (13.6 +ve charge) the overall charge is now wrong at -6-13.6=-19.6 must figure a way to solve this to get correct charges!