Hi, when I try to analyze protein secondary structures using 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. The gromacs version I used is 2018.3. The DSSP I download is latest version 3.0.10. Can you please help me how to solve this problem?
Thank you!
Yiran Qu
could you please post the error message you are getting in the console when you try to run the command? that way will be better for us to help you...
Hi, Mario!
Sure! Sorry about that.
The command I put are:
export DSSP=/fast/users/a1661804/gmx/bin/DSSP/xssp-3.0.10
1st: gmx do_dssp -f md_0_1.xtc -s md_0_1.tpr -sc Test.xvg -o Test.xpm -dt 10
2nd: gmx do_dssp -f md_0_1.xtc -s md_0_1.tpr -sc Test.xvg -o Test.xpm -dt 10 -ver 3
They both caused the following error.
The error message is:
-------------------------------------------------------
Program: gmx do_dssp, version 2018.3
Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668)
Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I also attach the screen snipping in the following for your information.
Thank you really much for help!
Make sure the binary works (and is right for your architecture) by executing the command shown by do_dssp interactively. The error message that do_dssp returns is a generic one, triggered by any type of failure by the dssp (xssp) binary.
do_dssp is simply a wrapper; it does no actual calculation. It writes a temporary file in PDB format, which is passed to the DSSP program (either called dssp or xssp, depending on the version). In your screenshots above, it is shown exactly what command is being attempted. Run that command (not via do_dssp) to see if the dssp/xssp binary works.
Justin Lemkul
Hi, Justin!
I'm a bit confused about what correct command I should input. As pictures shown, I input the command without do_dssp but looks not right. I check the DSSP website, and also not really sure how do I use dssp without from gromacs. Can you please suggest what command I should give?
Thank you really much!
It looks like your screenshots have disappeared for some reason so I can't be more specific, but again do_dssp prints out precisely what command it is trying to have dssp (xssp) execute. Run that. If you need more help, you'll have to post what command you gave, and what the actual output was. Saying something doesn't look right has no meaning to those of us who can't see your terminal window :)
Would you mind sharing what the solution was, so that when other people have this problem, they can refer to this thread?
Hi, Justin!
Sure! I double checked from very starting point when downloading DSSP and realized that there is binary of dssp missing. After I relocate, and set the environment variable in correct path, by using the command I mentioned before, it's working finally. Hope that helps:)
Use
gmx do_dssp -s... -f...
Part of your command belongs to the original version of DSSP software for only pdb structures.
I recommend you to install dssp v2, then copy it to the appropriate path.
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