I am trying to redock compounds on the protein's active site. But I am facing so many problems.
I am working on MOE2007.09 and want to calculate RMSD between the docked conformation of the ligand and the ligand in the complex structure of protein but I couldn't find any option to calculate RMSD.
If anyone can tell me the best possible way to calculate RMSD on MOE2007.09 or SVL and can give me command to calculate RMSD on SVL, I will be deeply grateful.
simply copy both ligand conformations from each complex and save them individually, without disturbing the conformations further, superimpose them.
super imposition can be done in MOE itself or else in easy way with Pymol.
you will get the RMSD very quickly.
hi everyone! i'm working with MOE 2014, and it gives the RMSD between the docked ligand and the co-cristalized.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA