Dear All, In my previous email the text in the message was not shown. Thats why I'm writing this again. I request to see the attachment of earlier message. I'm sorry for this!!
I have an disaccharide bound to a C-type lectin. The sequence of disaccharide is beta-galactose1-4beta-GlcNAc. The 3'OH and 4'OH of beta-galactose coordinate to the Ca2+ at the active site. FRET experiments have shown that if the disaccharide linkage is changed to beta-galactose1-3beta-GlcNAc then the binding affinity drops to 20 fold. I have attached both disaccharides in the figure. The left side residue is galactose and right side residue is N-Acetylgalactoseamine. . In order to do a free energy perturbation and find the relative free energy of binding for these two ligands, I have to slowly change the linkage from beta1-4 to beta1-3. If you look at the models of both disaccharides from the figure, to convert the beta 1-4 linked disaccharide to beta 1-3 linked disaccharide, I have to make the the C1 atom of Galactose attached to O4 of N-Acetylgalactoseamine as H atom and rest of the galactose residue to dummy atoms. On the other hand I have to grow the residue from H attached to O3 of N-acetylgalactoseamine to a galactose. The number of atoms involved is 21 atoms. Further the constraints I have is that the sugar should be bound in right conformation at the active site. So may be I need distance restraints. Does my approach make any sense? I have seen some papers by others where they add a fragment or delete a fragment between two ligands. But in my case the difference is the linkage between two residues. Thanks for your time in advance. Regards Sai
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php