Dear Amber user forum
I have a question on calculating the RMSD of the ligand for MD simulation.
One of the amber tutorials online suggests that "nofit" should be used when
calculating the RMSD for the ligand but not for the protein.
So an example of the prtaj input would look as below.
trajin MD_trajectory
reference reference_structure.pdb
rms reference mass :1-289
rms reference mass out ligand_rmsd.dat :290 nofit
My question is why we should use "nofit" for the ligand but not the protein?
If "nofit"is not specified, Is the RMSD for the ligand still legit or not?
If not, why?
Thanks a lot for your help!
Cheers
Marc
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Received on Mon Feb 22 2016 - 08:00:06 PST
