[gmx-users] do_dssp for coarse-grained trajectory

[Sandhyaa Subramanian]

Hi Tsjerk,
Thank you for the reply.
The coarse graining was done using MARTINI according to tutorials mentioned in their website.
Best, Sandhyaa 


 


     On Tuesday, 21 April 2015 12:46 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
   

 Hi Sandhyaa,
DSSP doesn't work on C-alpha only or coarse-grained trajectories. Can you maybe specify what coarse-grain FF you're using? It may be possible to use the tool 'backward' to convert it to atomistic.
Cheers,
Tsjerk
On Tue, Apr 21, 2015 at 6:48 AM, Sandhyaa Subramanian <sandysubram at yahoo.com> wrote:

Dear All,


I have a trajectory with the protein represented by C-Alpha atoms only. I was wondering if I could use ' do_dssp ' for predicting the secondary structure for this trajectory. When I tried to do so ( do_dssp -f trajca.xtc -s reference.pdb -o dssp_traj ) I got the following error -

Fatal error : Failed to execute command : Try specifying your dssp version with the -ver option 

I use GROMACS 4.6.5 and have set the environment for executing DSSP correctly. The reference pdb file (-s *.pdb) is also correct.  This command worked smoothly when I executed it for all-atom trajectories but when I want to execute for coarse-grain trajectory, it threw me the above error.

Please help.Thanking you.

Best, Sandhyaa



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