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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.
>