From: anu chandra <anu80125.gmail.com>
Date: Mon, 18 Jul 2016 18:27:26 +0100

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


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


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
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Received on Mon Jul 18 2016 - 10:30:03 PDT
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