[AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar

From: José Daniel Martinez <jmartinez.cicbiogune.es>
Date: Wed, 28 Nov 2018 16:50:38 +0000

Center of Excellence Severo Ochoa (2017-2021)

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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,


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Received on Wed Nov 28 2018 - 09:00:02 PST
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