I want to calculate the helix content, so which tool is much better? HSSP or DSSP?
AKBforever opened this issue · 6 comments
The download link in DSSP webpage of CMBI directed me to HSSP project. It confused me.
And I installed the latest version DSSP 3.1.4; however, when I use gromacs gmx do_dssp command, it keeps telling me specifying dssp version. I realized I can only give integer number, so I try -ver 3. But the error still there. Can you please help me how to solve this problem?
Could you give the exact output from gromacs? DSSP 3.1.4 should work.
Also, you submitted this issue on the hssp repository, but did you download dssp from the dssp repository?
https://github.com/cmbi/dssp/releases/tag/3.1.4
(it has moved)
Could you give the exact output from gromacs? DSSP 3.1.4 should work.
Also, you submitted this issue on the hssp repository, but did you download dssp from the dssp repository?
https://github.com/cmbi/dssp/releases/tag/3.1.4(it has moved)
Dear @cbaakman , thanks for your reply. Yes, I downloaded the DSSP 3.1.4 from the DSSP repository; but when I tried running DSSP, this error in the following snapshot occurred. I don't know how to solve this problem, the only way is to use the old version of DSSP?
Have you tried to run the mkdssp executable itself and see if it had any outcome? I'd like to know what happens when you run the mkdssp executable on the pdb file that you were using in gromacs.
Also, you can tell gromacs which mkdssp executable to use. That's described here:
http://manual.gromacs.org/5.1/onlinehelp/gmx-do_dssp.html
the reason of your problem may be that you use a lower version of GMX. From my pratical situation,I installed dssp on my Ubuntu 18.04 with GMX 2019.4 It run perfectly,but I have to export the path because dssp's name is mkdssp,not dssp in the path-/usr/local/bin/
The last dssp version able to handle gromacs produced pdb files is 3.0.11... from 3.1.0 it cannot handle them as they miss some information :/
I attach one of the offending files
The same happens with dssp-4
https://gitlab.com/gromacs/gromacs/-/issues/4129
Dear users,
this repository is discontinued. Please use:
https://github.com/PDB-REDO/dssp