Dear Xuewu, Not easily, I’m afraid. In theory heparin *could* be handled by the GLYCAM force field ISOLDE uses for glycosylation sites, but its template scheme is entirely different from the residue representation in the PDB - in GLYCAM, each sulfate and the reducing-terminal hydroxyl are treated as extra residues tacked on to the sugars. Would take a bit of careful special-purpose code to support. If your heparin chain is reasonably short, you might get reasonable results by treating it as a single large residue and parameterising with the “isolde param” command. All the best, Tristan On Sat, 4 Nov 2023 at 01:22, Xuewu Zhang via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Tristan, Can ISOLDE handle heparin molecules now? I tried to simulate a heparin chain, it says one residue is not properly parametrized. I am using ISOLDE in Chimerax 1.6. Thanks, Xuewu _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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