Hello to everyone,
I would like to ‘properly’ describe a trimannoside which is fluorinated at position 2 (the fluorine substitutes the OH) in each monomer. I know that the ‘easiest’ way of doing so is just by using GAFF… but in that case I would lose all the special sugar-related chemistry that is modeled in GLYCAM.
For that purpose, I thought of adding a .frcmod file to use in combination with GLYCAM force field. In such .frcmod file, I would include the necessary parameters from GAFF (gaff2.dat). I would like to combine both force fields, if possible, in order to keep the exo-anomeric effects modeled in GLYCAM while introducing the GAFF 'standard' parameters describing the C-F interaction ‘environment’.
Reading the manual I realized that I would need to adapt probably lots of things for this not be a complete disaster…
Of course I know this would be a (very) rude simplification, but I just wanted to ask which will be your recommendation for approaching this issue.
Thanks a lot in advance,