[gmx-users] DSSP => MainChain+H group ?

[Chih-Ying Lin]

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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