[gmx-users] do_dssp question

[Justin A. Lemkul]

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

> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================