[gmx-users] do_dssp for coarse-grained trajectory

Sandhyaa Subramanian sandysubram at yahoo.com
Tue Apr 21 06:54:40 CEST 2015

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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