[gmx-users] make_ndx for do_dssp

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> Hello, I want to check the secondary structure of protein at particular
> residues. Since dssp needs all main chain atoms, does the following command
> at the make_ndx prompt makes the correct index file? 

You can answer that yourself by looking at the resulting index file.

> 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
> 

To get these groups to merge, I think you probably need to do 5 & r 1 | ...

-Justin

> (Main chain atom of particular residues). regards,
> 
> Paymon
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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