[AMBER] How to apply GLYCAM Parameters

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Sun, 3 Jan 2021 15:45:07 -0500

Dear Amber Community,

I have a glycolipid ligand I want to model. I can easily generate GAFF2 parameters for it, but I thought using the GLYCAM force field would be more appropriate. If I load GLYCAM into leap, and then the PDB of the glycolipid, none of the atoms are recognized. Do I need to assign the atom types by hand, or is there an easier approach? If I should proceed by hand, can you please direct me to what files I should look at to assign the atom types?

I noticed in the archive that someone asked a related question of how to assign parameters for a glycolipid, but the answer was not very satisfactory. I’ve looked through the literature, and wrote to a few people who apparently figured out how to do what I am attempting, but while I am awaiting responses on that front, I wanted to also pose the question here.


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Received on Sun Jan 03 2021 - 13:00:02 PST
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