[gmx-users] secondary structure

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 10 15:32:25 CEST 2008

s lal badshah wrote:
> Hi All,
> I want to study and calculate the secondary structure as a function of 
> time of my MD simulated protein. I have no DSSP installed but will use 
> VMD for this.Can any one suggest me which files of MD simulation 
> output I should used? or I need to develop PDB file of the whole MD 
> simulation trajectories?
> Hoping for an early guidance

Sounds like more trouble than it's worth.  DSSP is free, just fill out 
the license and download it...Just my $0.02.


> M.Phil
> NCE in Physical Chemistry,
> University of Peshawar.
> NWFP,Pakistan.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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