[gmx-users] make_ndx for do_dssp

[Paymon Pirzadeh]

Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?

Paymon

On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
> 
> 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
> > 
> 
> -- 
> ========================================
> 
> 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
> 
> ========================================