Chetan kumar Meena

16 Questions 17 Answers 0 Followers

Questions related from Chetan kumar Meena

How to perform molecular dynamics simulation of Protein-RNA complex at different pH condition??

Hi, I want to perform molecular dynamics simulation of protein-RNA complex at deifferent pH condition in gromacs. When I am using Amber force field, It is not detecting protonated residues while...

05 May 2017 8,387 4 View

Can anyone tell me protein's name whose three dimensional structure contains Gold atoms?

I want three-dimensional coordinates for Gold atom.

11 November 2015 7,731 1 View

How do I perform protein-ligand simulation in gromacs with gold atoms?

I want to run protein-Ligand simulation where gold atoms are ligand. Gromacs is showing error for that. I tried to use Prodrug server also, but it is not generating coordinates for gold...

11 November 2015 4,400 7 View

How can I build the virion capsid from single coat protein?

I am having the full-length homotrimer coat protein's predicted model. I want to rebuild virion capsid (Icosahedral virion) by using this homotrimer. Capsid structure of this virion is available...

11 November 2015 9,317 3 View

Is there any kind of change in pH of cell while it is dying due to viral infection?

Viruses are using cell machinery for its amplification. After enough number of replication cycle it leaves cell and attack next cell. Is there any chance of changing pH of that infected cell...

01 January 2015 4,281 11 View

How can we calculate the volume of a particular domain in simulation trajectory in gromacs?

I want to check the agonist and antagonist effect of ligands on the same protein by doing simulation studies. Protein functioning is a result of conformational changes in protein structure and...

08 August 2014 5,638 4 View

What is the relation between stability of protein and Gibbs free energy?

If conformational changes are occurring in protein structure then how will it effect Gibbs free energy of that particular protein?

11 November 2013 8,671 14 View

How to predict protein structure along with dsRNA?

I want to model one protein structure along with Double strand RNA molecule. I tried to dock this RNA in protein with the help of HADDOCK server but it is not giving the exact pose which I needed...

08 August 2013 1,697 4 View

How do I infer energy landscape in Dihedral Principle Component analysis in Gromacs?

I am performing MDS to find out conformational changes in protein structure. To verify that result, I have done Dihedral Principle Component analysis (DPCA). I got the result up to energy...

07 July 2013 4,515 0 View

I am facing some problems while running a pH dependent simulation of homotrimer. Can anyone help me to solve the given error below?

Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.

06 June 2013 2,610 4 View

How to do multi-chain and multi-template modeling at same time in modeller?

I want to do multi-chain modeling by using more than one template at one time. How should I do this? Do I need to change model_multiple python script or to change model_multichain script?

06 June 2013 9,007 2 View

What is cross correlation and auto-correlation in image processing?

In the processing of TEM images, we are using term auto correlation and cross correlation. What does that meaning meaning?

04 April 2013 5,946 1 View

Running simulation at different pH values.

I want to check the conformational differences in proteins at different pH values, can anyone give me some suggestions about how to do this?

03 March 2013 8,713 1 View

Is there any bacterial species which enhances the fertility of land?

Is there any bacterial species which enhances the fertility of land? That bacteria should have the capacity to convert sand from solid to amorphous.

02 February 2013 7,383 12 View

Cases of cancer are increasing very rapidly. Is there any possibility that these are increasing because of uncontrolled use of medicines.

Nowadays people are using so many medicines without any prescription. Every drug has their own side effects. Is it possible that this increases cancer cases.

02 February 2013 6,346 11 View

How can we study gene silencing process in viruses by studying genome and coat protein interaction?

01 January 2013 4,041 2 View