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

[Justin A. Lemkul]

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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