Dear All,
It is not clear from manual how to analyse my requirements after simulation.
Could you please help me in the following regards:
1> How to get the graph on "occupancy of hydrogen bond interactions of
ligands throughout 5 ns simulation" and "occupancy of a particular
salt-bridge throughout the simulation" ?
2> I want to get a graph of the distances of some particular co-factor
atoms and active site residues atoms throughout the simulation.
Suppose I want the distance graph between DPM:C9B and Arg7:CA for total
simulation.
3> Average hydrogen bond distance between active site residues and ligand.
4> RMSD of some particular residues from its initial structure.
5> Total formal charge residing at active site throughout the
simulation (All +vely charge and -vely charge residues within 15 A
radius of active site will be considered).
It would be a great help if you could kindly give some sample commands
for these analysis.
Sorry for lots of questions.
Thank You.
Regards,
Sukesh
--
Sukesh Chandra Gain
TCS Innovation Labs
Tata Consultancy Services Ltd.
'Deccan Park', Madhapur
Hyderabad 500081
Phone: +91 40 6667 3572
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