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GLYCAM-L  November 2018

GLYCAM-L November 2018

Subject:

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

From:

"J. Martinez" <[log in to unmask]>

Reply-To:

Users of GLYCAM & GLYCAM-Web <[log in to unmask]>

Date:

Thu, 29 Nov 2018 04:55:59 -0500

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text/plain

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text/plain (10 lines)

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.

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