I have a native and mutant PDB files. How to find the percentage of alpha helix, beta sheet, turns etc., from the pdb file (not with the FASTA sequence)
You can use the STRIDE program implemented in VMD package. For that, you will need to have the PDB coordinates. It is not going to give you the percentage numerically (in %), but you may still be able to determine it from the graphs, by estimating the number of residues forming each secondary structure.
Reference: Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.