[gmx-users] Residue specific secondary structure analysis

[Justin A. Lemkul]

Biswaranjan Meher wrote:
> Dear All,
> 
> I have a simple querry regarding the secondary structure analysis.
> Using my_dssp I have done the secondary structure analysis for my 
> protein (all residues) of interest.
> But I want to show the secondary structural changes for a / few 
> particular residues in the protein.
> Is it possible to create a  .xpm file for  a single residue over the 
> whole period of the simulation ?  Or there is some tricky way to do that ?
> If yes, can any body suggest me in this regard ?
> 

As with all Gromacs analysis tools, do_dssp can be passed an index file with the 
subset of atoms of interest.

-Justin

> Thanks in advance for your kind suggestion.
> 
> with regards
> BR Meher
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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