Run DSSP with GROMACS 4.5.5 on Red Hat Linux

UPDATE

A new version of GROMACS (4.6 series) has been released since this post was written. Please try installing the latest version of GROMACS before attempting the steps in this post.

Fixing GROMACS

There is a bug in the do_dsspcommand in GROMACS 4.5.5 that prevents the analysis of secondary structure using DSSP . Attempting to rundo_dssp will result in a segmentation fault. The bug has been patched since 4.5.5, but this version has not been released (see this post on the GROMACS mailing list). To get the patched version, follow the instructions from this post.

git clone git://git.gromacs.org/gromacs.git
git checkout --track -b release-4-5-patches origin/release-4-5-patches

On our Red Hat Enterprise Linux cluster, I built the patched version of GROMACS and linked it against FFTW3. Here is the FFTW3 configure command that I used:

./configure --prefix=/apps/fftw3_shared_intel_openmpi --enable-float --enable-mpi --enable-openmp --enable-threads --enable-shared

I used the following command to configure GROMACS:

CPPFLAGS="-I/apps/fftw3_shared_intel_openmpi/include" LDFLAGS="-L/apps/fftw3_shared_intel_openmpi/lib" ./configure --enable-mpi --prefix=/apps/gromacs-4.5.5-patched-intel-openmpi-fftw3/

Note that we have adopted a convention of installing non-system software in the /apps directory instead of one of the conventional Linux directories. This allows us to keep our base RHEL system clean and stable.

DSSP

NOTE: This section is out of date. The old version of DSSP is no longer available. I would assume that GROMACS has been updated to work with the new DSSP by now, but I haven’t used it in many years.

There are two versions of DSSP. GROMACS will only work with the oldversion of DSSP! Download the old version of DSSP from this site. I downloaded the Linux binary executable, and it worked fine on our system. You’ll have to change the file permissions to make it executable after you download it. Make sure you set the environment variableDSSP to point to the DSSP binary, as described in the do_dssp manual page.

Comments

Comment #1 by Amine

Amine - Nov 0, 2012

Thank you for this post i guess i have the same problem i’m using the ubuntu package of Gromacs v4.5.5, and dssp executable version 4.0.2 dssp-2.0.4-linux-amd64 when i run the command: do_dssp -f traj_final.xtc -s PON1md1.tpr -sc scount.xvg -o ss.xpm -dt 10 i get the follwing error: ——————————————————- Program do_dssp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddFKdvmZ ddMpvdud > /dev/null 2> /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ——————————————————- Can you please help my fix this problem Thank you

Comment #2 by craig

craig - Nov 1, 2012

Amine, Your error message looks a little different from the one I had. In my case, DSSP had a segmentation fault, while in your case, GROMACS seems to be unable to run DSSP. Is DSSP installed on your system in/usr/local/bin/dssp ? Once you solve that problem you will probably find the segmentation fault that I encountered. Then follow the steps described in this post to download and install the newest version of GROMACS. Craig

Comment #3 by T

T - May 5, 2013

Thank you this was super helpful! I just couldn’t find the old DSSP version!

Comment #4 by Craig

Craig - May 5, 2013

You are welcome! Thank you for letting me know that my post was helpful.

Comment #5 by shika

shika - Jun 0, 2013

i’m still cant used the do-dssp..im having the same problem with your which is segmentation fault after i run the do_dssp.i’m following your step but there are some error after i run git checkout.can u help me?thanks in advance

Comment #6 by Craig

Craig - Jul 1, 2013

GROMACS 4.6.2 has been released, and the do_dssp bug may have been fixed. Please download the latest GROMACS release and try that first.

Comment #7 by uma

uma - Dec 1, 2013

hi i am new to gromacs. i want to analyze the secondary structure of protein. for that i tried with do_dssp. but it shows error. DSSP executable (usr/local/bin/dssp) does not exist. use setenv dssp command. while attempting this setenv command, i am facing error: bash setenv command not found. in my gromacs, bin folder do_dssp executable is there? what can i do?

Comment #8 by Craig

Craig - Jan 0, 2014

Uma, “setenv” is not a valid bash command (it is used in a different shell called tcsh). Environment variables in bash are set as follows: export DSSP=’/usr/local/bin/dssp’ Note that this variable only lasts as long as the shell is running. If you want to set that variable every time you start a new shell, you will have to add that line to your .bashrc file.

Comment #9 by kesavan

kesavan - Mar 5, 2015

hi , im just using gromacs 4.5.5 version and found the same segmentation fault in my system. i tried to follow ur command but its not working showing a fatal: unable to connect to git.gromacs.org: git.gromacs.org[0: 130.237.25.132]: errno=Connection timed out could u please help me to sort out this problem

Comment #10 by Craig

Craig - Mar 5, 2015

The git command still works for me, so there must be a problem with your computer’s connection to the Internet. Note that a new official version of GROMACS has been released, so the best solution is to upgrade to a stable release instead of using an old development version.

Comment #11 by jaish

jaish - Jan 5, 2022

thanks CRAIG . but I can’t download old dssp from internert because i think their old server is no more on internet. it would be great help for me if you provide me old dssp executable through drive link or you can send me that executable by mail jaishuddin9@gmail.com

Comment #12 by craig

craig - Jan 5, 2022

All you have to do is google “DSSP” to find the new site, which is https://swift.cmbi.umcn.nl/gv/dssp/

Comment #13 by Jaish

Jaish - Jan 5, 2022

Yes already i have gone through the link you given.but there old version of dssp 2.0.0/2.0.4 is not available.

Comment #14 by Jaish

Jaish - Jan 5, 2022

@CRAIG please help me if possible.i’m troubleshooting with this problem for a long time