Atul Pawar

7 Questions 10 Answers 0 Followers

Questions related from Atul Pawar

Can I do simulation of the PDB structure ?

I want to know, whether a particular PDB structure has any calcium binding pockets or residues. It is already bound to a calcium ion in PDB, so I want to simulate it at a particular conc. of...

17 April 2013 1,043 9 View

Residence time of calcium ion in proteins

Can someone shed some light on the residence time for a calcium ion bound to protein residue? I need the information for MD simulation. I have read a few papers where it is mentioned to be around...

10 March 2013 1,230 0 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...

07 March 2013 6,759 9 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...

25 January 2013 7,270 12 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...

25 January 2013 1,814 1 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...

21 January 2013 9,379 3 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...

20 January 2013 2,381 5 View