Hello AMBER users,
After a 50 ns long simulation, I am trying to analyse the change in ligand
structure and binding pose from it initial docked pose in a protein-ligand
complex. For this, I am trying to calculate the ligand rmsd from its
initial docked pose using following different cpptraj commands,
1. here I first align the protein-ligand complex and then do a no-fit rmsd
for ligand,
*****************************************************
trajin ../1md.nc
trajin ../2md.nc
autoimage
reference eq.crd
rms reference :1-451 # 1-450 for protein and 451 is ligand
rms reference out ligand_nofit.dat time 2 :451&!.H= nofit
***********************************************************
This produce an average ligand rmsd of about 5 angstroms
2. My second try was to do a straight-forward rmsd calculation for ligand
alone, without any prior aligning of protein-ligand complex ( presuming
that ligand align itself)
************************************************************
trajin ../1md.nc
trajin ../2md.nc
autoimage
reference eq.crd
rms reference out ligandrmsd.dat time 2 :451&!.H=
***************************************************************
The calculates average rmsd here was about 1.5 angstroms.
Now, I just wonder which of above is capturing the actual scenario.
Any suggestions would be highly appreciated
Many thanks
Anu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 18 2016 - 10:30:03 PDT
