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

From: Soumendranath Bhakat <>
Date: Wed, 16 Jul 2014 14:10:22 +0200

I would suggest you use multiple analysis approach.

1. Firstly you can calculated distance among residues during the simulation
time to capture the shift. Say for example distance between CA of Asp120
and another neighbouring group which can capture the shift. Use CPPTRAJ
distance script for that.

2. Dump PDBs at different interval using CPPTRAJ script to check evolution
of Asp120 and its shift in real time. Use this script.

trajin md2_dry.mdcrd
outtraj snapshot10.pdb onlyframes 10000 (this implies sanpshot10.pdb
corresponds to 10ns and you can dump at any interval if you save
trajectories in every 1ps)

3. Do a Residue Interaction Analysis otherwise known as RIN on snapshots
dumped. Say for example in 10ns time theere is connection between Asp120
and X21 and you get the edge value which signifies the power of connection.
Now in 30ns that connection value is less that signifies there is a shift
which will be backed up the distance calculation. Use Cytoscape and
RINAnalyzer plugin for that.


On Wed, Jul 16, 2014 at 2:00 PM, anu chandra <> wrote:

> 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
> Sincerely
> Anu
> _______________________________________________
> AMBER mailing list

Thanks & Regards;
Soumendranath Bhakat
AMBER mailing list
Received on Wed Jul 16 2014 - 05:30:03 PDT
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