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'
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?
The DSSP algorithm looks for mainchain hydrogen bonding patterns to assign
secondary structure. The program hangs if you feed it unnecessary information.
As you've quoted me above, side chains don't categorize secondary structure,
backbone hydrogen bonds and torsions define secondary structure.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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