[gmx-users] secondary structure
Mark.Abraham at anu.edu.au
Tue Jun 10 15:58:48 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
VMD reads any GROMACS-format trajectory natively into a suitable
structure file, e.g. the .gro file produced by your simulation.
Searching the wiki to find http://wiki.gromacs.org/index.php/VMD would
have told you this. Anyway, then do whatever you like with VMD from there.
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