[gmx-users] do_dssp for coarse-grained trajectory

Sandhyaa Subramanian sandysubram at yahoo.com
Tue Apr 21 09:51:35 CEST 2015

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.
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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