Sandeep Singh

5 Questions 54 Answers 0 Followers

Questions related from Sandeep Singh

Can anyone guide me how to select best representative structure from ensemble of structures obtained after performing MD

I have performed ab initio folding of a small peptide structure using MD and have got 1000 structures in the MD trajectory of 1 nanosecond ( 1 structure after every picosecond). Please suggest me...

03 March 2016 4,925 16 View

[SOLVED]In protein ligand simulation using gromacs, how can I fix starting point of ligand close to protein active site?

When I start a protein ligand simulation in gromacs, my ligand molecule is far away from protein molecule. Even after 5 ns simulation, the situation is same. I want that my ligand molecule should...

03 March 2014 9,162 12 View

How to add non-natural amino acids in peptide for simulation in Gromacs ?

I have a peptide and I want to add non-natural amino acids in this peptide. After incorporating non-natural amino acid in peptide, I want to do simulation of that peptide in gromacs. Although I...

02 February 2014 6,905 6 View

[SOLVED]Can anyone suggest how to minimize phi and psi torsion angles based on ramachandran plot?

I have a pdb file which has distorted tertiary structure with serious steric clash within backbone. This pdb file was generated by assigning some phi and psi values to each residue of a protein...

11 November 2013 3,748 10 View

How to use self made BLOSUM matrix in standalone blast?

I have my own self made BLOSUM matrix (made for a specific problem which is not being solved by conventional BLOSUM/PAM matrices). I want to use it in standalone BLAST. Although BLAST has -M...

11 November 2012 9,382 1 View