[AMBER] How to generate the .mol2 and .frcmod files for a carbohydrate with GLYCAM06 atom types in Antechamber

From: Bhat Zahoor <dr.zahoor11.gmail.com>
Date: Sun, 7 Nov 2021 15:18:23 +0530

Dear Amber Community,

I am supposed to simulate Protein - ligand complex wherein the ligand is a
carbohydrate. I had used Antechamber with GAFF force field (giving gaff
atom types) to generate .mol2 and frcmod files for this ligand to be used
in Leap. Then in the Leap, I had called in GLYCAM_06j-1 force field along
with the ff14SB force field but I don't think the ligand is being taken
care off by the GLYCAM_06j-1 force field because of the atom types and the
partial charge (generated using GAFF) as it flies away after a few nano
second simulation.

Now, I want to generate the .mol2 and .frcmod files for this ligand having
GLYCAM_06j-1 atom types and partial charges but I have not got any clue how
to do it. Any help would be appreciated.

Thank you.
*Zahoor Ahmad Bhat*
Research Scholar
Multidisciplinary Centre for Advanced Research and Studies
Jamia Millia Islamia
New Delhi - 110025
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Received on Sun Nov 07 2021 - 02:00:02 PST
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