[AMBER] calculate ligand RMSD for MD simulations; nofit or not?

From: Marc Zhang <marczhang_md.zoho.com>
Date: Mon, 22 Feb 2016 16:52:23 +0100

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

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 22 2016 - 08:00:06 PST
Custom Search