I am using GLYCAM in AMBER to conduct simulations of glycans. But the system I am working on contains modified monosaccharide residues GlcNAc6S. Basically, there is a sulfate group attached to C6 of GlcNAc. Any solutions to this situation? Thanks in advance!
Zhaoxi Sun Thanks for your answer! Fortunately, I found the force field for the sulfate group in GLYCAM. It is stored as SO3. So, there is no trouble in generating the parameters.
As a side note, I should make my original question more specific. The problem I encountered is that the modified monosaccharide residue connects more than 2 other residues. (OMG the high structural variation of oligosaccharides...) I know how to make modified residues with prepgen and residuegen. But both seem to have a requirement to have equal or less than two dangling bonds, meaning they are not optimal for making residues that connect more than 2 other residues. Any ideas on solving this problem?
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