Hi 1.type => do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg Select a group: 1 Selected 1: 'Protein'
As Justin said: "Don't analyze Protein. Think about it - you're looking at mainchain hydrogen bonds. Side chains and such don't matter for DSSP. Use the MainChain+H group for analysis." Why? What is the difference? Thank you Lin Chih-Ying Lin wrote: > HI > > 1. > type => > do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc > secondary-structure.xvg > > Select a group: 1 > Selected 1: 'Protein' Don't analyze Protein. Think about it - you're looking at mainchain hydrogen bonds. Side chains and such don't matter for DSSP. Use the MainChain+H group for analysis. -Justin
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