[gmx-users] do_dssp for coarse-grained trajectory

[Tsjerk Wassenaar]

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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-- 
Tsjerk A. Wassenaar, Ph.D.