[gmx-users] free energy calculations for two ligands

[Sai Kumar Ramadugu]

Dear All,
   I have a trimeric protein system which binds to two different ligands.
The ligands are oligosaccharides. The difference between the two is first
ligand has beta 1-4 linkage and the second ligand has beta 1-3 linkage
between Galactose (Gal) and N-Acetyl Glucosamine (GlcNAc). Since the linkage
changes I have changes in atoms, bonds, pairs, angles and dihedrals.
In the pair and dihedrals, some of the pairs are present in the first ligand
and not in the second ligand. How do I make the topology for the change from
ligand A to ligand B in the free energy simulations? The same is the case
with dihedrals. Angles, bonds and atoms have no problem. Can someone please
help me in this regard?

Thanks for your time.

Regards
Sai
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