I am following Zhang (2015) Understanding the impact of Fc glycosylation on its conformational changes by molecular dynamics simulations and bioinformatics https://bit.ly/2Hi6TYT .
I have created topology files for the polypeptide chain of my glycoprotein using GROMACS and, separately, ANTECHAMBER and ACPYPE to generate a separate topology file for the glycan, as described in the paper.
After creating the topologies, I deleted the appropriate hydrogens (and associated bonds, pairs, angles, and dihedrals) on the glycan C1 and the Asn side-chain N so that I can define the C-N bond.
How do I define the protein-glycan C-N bond, though? I can't find information on how to link two subunits of one molecule together.
You might be able to add an entry in specbond.dat that defines the bond between those residues, otherwise construct an .rtp entry for a new residue that has the protein-glycan entity in its entirety.
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