[AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement

From: anu chandra <anu80125.gmail.com>
Date: Wed, 16 Jul 2014 17:30:25 +0530

Dear amber users,

I am working with MD simulation of protein-ligand system. From literature,
I came to know that a residues, say ASP120, in the binding site shift about
5 angstroms during ligand binding. I would like to capture this shift from
my simulation. Is there a quantitative analysis tool in PTRAJ/CPPTRAJ,
which can explain the shift in angstroms itself?. I can try with evolution
of dihedral angle about CA-CB plane, but it wont help me to see the extend
of shift?. Waiting for your valuable reply

Thanks in advance

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Received on Wed Jul 16 2014 - 05:30:02 PDT
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