Kirill Bessonov wrote:
I have used do_dssp program to analyze secondary structure during
simulation of DMPC/DMPE. But I am not clear on installation of dssp.
The program seems to work, I have set all the environmental variables so
that dssp binary is seen in /home/DSSP directory, but I am not sure if I
need to download the database of dssp files from the internet to make
this program work.
No libraries or other databases are necessary.
There are 14 residues in your selected group
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
trn version: GMX_trn_file (single precision)
Reading frame 0 time 52.000
Back Off! I just backed up ddoSxMLN to ./#ddoSxMLN.1#
Last frame 0 time 52.000
100%
And I get ss.xps file that when I open it in image viewer is just a blue
line.
Then you've got a consistently helical protein. It could be that your axes are
skewed a bit, but you can change proportions using a .m2p file. An example is
available in the online manual.
How should I properly setup the program and whether it will give me
%alpha helicity over the course of the trajectory, thank you
To calculate % helicity, make use of scount.xvg (the other default output).
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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