Hi Dan,

I have only vague advice for you. I have mixed GAFF and GLYCAM using a frcmod where I picked the best parameters I could find. However the accuracy required for the application was quite low (very simplistic modeling) so I could defend what I did. You'll have to figure that out based on what you plan to use the results for. You can describe the project here if you like. To do it "properly" you must develop charges as done for GLYCAM. I see you've been recommended here from this http://archive.ambermd.org/201811/0288.html.

Xiao is probably best suited to answering on how to go about developing charges.

Oliver

On Thu, Nov 29, 2018 at 11:05 AM J. Martinez <[log in to unmask]> wrote:

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,

Dan.