Hi everyone
I have a protein-ligand complex. The protein has 305 residues and the ligand is the residue number 306.
When I calculate the RMSD with cpptraj, what should I tell it to do, calculate the RMSD with the 306 total amino acids or just the ligand?
I use this script:
> parm 6W63-DEX.prmtop
> trajin 6W63-DEX-NVT.nc
> rms ToFirst :1-306 fist out rmsd1.agr mass
> run
Thanks in advance
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Received on Thu Sep 14 2023 - 05:30:02 PDT
