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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...
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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...
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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...
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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...
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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...
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