Atul Pawar

9 Questions 16 Answers 0 Followers

Questions related from Atul Pawar

Number of calcium ions for my system

I have to simulate protein in 400mM calcium ion conc. I will neutralise the system with chloride ions. My system now has 265 protein residues and 18610 water (SPC) molecules. How many calcium do...

04 April 2013 6,027 2 View

Protein simulation in the presence of calcium (400nM)

I want to do an MD simulation in gromacs on a protein to study the effects of calcium conc (around 400 nM). I want a good protocol to introduce calcium ions in to the system to have the desired...

03 March 2013 5,857 10 View

Force fields in GROMACS 4.5.5

I want to have comprehensive information on the force fields present in gromacs, in the PDB2GMX command. Any article on comparative analysis of ff will be welcomed. Also, info. on which ff to use...

03 March 2013 9,442 2 View

3 residues are outliers in a ramachandran plot

I have done homology modelling and then refined the model with MD in gromacs. Then I did clustering of trajectories and selected the average structure of the model. Finally I did energy...

01 January 2013 4,259 13 View

B-factor from PDB and RMS fluctuation graph from MD

I have MD simulated a homology model in gromacs. I have obtained an RMS fluctuation graph for the same. Can this graph be compared with a PDB file which has b-factors generated during X-ray...

01 January 2013 746 1 View

Protein modeled with I-TASSER server.

But 2 of its disulphide bonds out of 5 are missing and I have information on the disulphide bonds and want to include them in to model. I also want to do Molecular dynamics on protein with...

01 January 2013 6,091 2 View

Molecular dynamics of protein in gromacs in presence of calcium.

I want to study the structure changes of proteins in presence and absence of calcium ion. The calcium concentration would be 400mM and the phenomenon of interest is sec. structure changes, local...

01 January 2013 4,497 8 View

I have done a molecular dynamics simulation in gromacs on a protein and want to find phi and psi angles for a residue.

I want to get the psi and phi angles on a particular residue and plot them on ramachandran plot. I went through some tutorials and was informed to use ndx file for that. But can someone give me an...

01 January 2013 4,379 6 View

How to find potential inhibitors for a protease.

i have a papain-like protease but having Chymotrypsin-like activity due to non-canonical active site Serine. I have to find inhibitors for this protease with in-silico methods. Can i dock...

01 January 2013 5,979 3 View