I did try to use CGenFF to obtain imidazole ring associated parameters. But CGenFF website gave param penalty of 187.500 and charge penalty of 47.153 for analogue parameters.
(1) I can use FFTK within VMD or follow charmm guidelines to generate parameters and charges for the whole chromophore from scratch.
(2) Use analogue parameters from phenol derivatives for deprotonated tyrosine and, use FFTK or follow charmm guidelines to derive charges and parameters for the imidazole ring
(3) Use analogue parameters from phenol derivatives for deprotonated tyrosine and, all other parameters taking from already published work (https://doi.org/10.1021/jp014476w
(4) Just simply use already published parameters for the whole chromophore along with C36m for the rest of the protein and see if chromophore within GFP matches experimental observations for validation.
If I am to chose from these four options, which one will you recommend?.
Also, I am wondering, what limits me using parameters derived for C22 to be used in C36? especially considering parameterization guidelines for novel residues are the same for C22 and C36 (please correct me if it is not)
p.s-sorry for the long request, I wish to know how exactly charmm developers look at this issue for me to learn from it. I am a bit reluctant to develop parameters for a system like this, especially when parameters from Reuter et al itself was never incorporated to charmm though it has been cited a lot.