Deepasree K.

6 Questions 5 Answers 0 Followers

Questions related from Deepasree K.

I did the hydrogen bond analysis for a100ns MD simulation of a protein-ligand complex. Can anyone help me to analyze the graph?

A major portion of the graph obtained was filled with black background instead of black lines but the no. of hydrogen bonds were displayed. Kindly help me to understand what that means.

10 August 2023 7,173 0 View

Is it possible for a ligand to have greater energy contribution value than a protein's amino acid residues?

When I performed an energy decomposition per residue analysis, it was observed that ligand exhibited a significant energy contribution value when compared to the amino acid residue. In fact the...

28 March 2023 6,852 0 View

What to do if power goes out while performing MD run?

I was running a 100ns MD simulation and in the process the system was shut due to power cut. Is there any way to resume the simulation?

17 February 2023 8,158 3 View

"swig/python detected a memory leak of type 'bhtree *', no destructor found". What does this mean?

While docking using AutodockTools 1.5.7, this msg pops up in the command prompt while inserting protein, but grid parameter files and the binding affinity results are perfectly generated. Is it ok...

08 February 2023 5,114 1 View

How to select active site residues for site-specific docking?

For some of my proteins, active site residues are not mentioned in the literature. So I looked into some online tools which generated more than 10 active site residues. Is it okay to use those...

31 January 2023 1,854 3 View

Is energy minimization of ligand essential before docking?

I had energy minimized few ligands of my study using Argus Lab software and used those energy minimized ligands for docking. But then ligands appeared as disconnected parts in AutoDockTools. So, I...

31 January 2023 2,625 4 View