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