Error in gmx do_dssp

GROMACS version:2020.1.1
GROMACS modification:

I got a segmentation error when I ran gmx do_dssp command.
Can anyone support me to solve this ?

You may need to specify the appropriate DSSP version, e.g. -ver 1 or -ver 2 based on what binary you have.

Also note that making a selection from the whole protein is not correct for do_dssp, you should derive your index group from MainChain+H, which is what the DSSP algorithm needs. I don’t know if it’s still the case, but a long time ago, the program crashed if you provided other atoms like sidechains.

Dear @jalemkul ,

Thank you for your suggestion. I have DSSP version 4.0.4, I tried but I got the same error. Do you have any other recommendations ?

I have no idea if DSSP 4 will be compatible, but you should definitely be using a newer version of GROMACS. 5.1.1 is not supported and could be buggy, but I don’t know. Make sure your DSSP binary actually works by running it on a PDB file to see what happens.

Dear @jalemkul ,
I used “sudo apt install dssp” command to install dssp and it automatically install the latest version. Do you know how to install dssp version 2 ?

You’d have to do it from source. That code has moved around so much, I don’t know where that is any more or if anyone makes it available.

May I know if the command runs properly, I have been waiting for the result for quite a long time.
Please see the attachment

Looks fine. The program takes forever to run because it’s just dumping a frame to disk, running the external DSSP binary on it, storing output, then replacing the file. It’s incredibly slow.

Plz, see the solution uploaded here.