Thank you for your response sir, but i have checked with gromacs mailing list but i am unable to solve these problem. I am following the follwing protocol, will you please check and help me to rectify this problem.

1. First of all i downloaded the dssp-2.0.4-linux-i386 file from ftp://ftp.cmbi.ru.nl/pub/software/dssp/ and saved in the location of usr/local/bin directory

2. I rename the execution file name as dssp and saved in usr/local/bin/dssp directory

3. I set the env variable: export DSSP=usr/local/bin/dssp/dssp

5. and trying to run the do_dssp command from /usr/local/gromacs/my_folder_name

but i am I am getting error like this

Program do_dssp, VERSION 4.5.3

Source code file: do_dssp.c, line: 521

Fatal error:

Failed to execute command: /usr/local/bin/dssp -na ddFx6MlC ddFcs4xm > /dev/null 2> /dev/null

Hello. You don't need to specify the path, because /usr/local/bin is already accounted for. To test this, write on your shell:

$ dssp -h

If you get the correct output, you can run the 'do_dssp' command easily without any more configurations

@Ricardo and Stephane, when i am giving command $ dssp -h it is showing -bash command not found. But when i am giving comand $dssp.exe -h it is running and asking any key to continue...Please suggest. I use this command using "/" also.

So, you have to rename 'dssp.exe' to 'dssp' because GROMACS detects by default the command 'dssp'. If you want to use dssp.exe or cannot rename dssp.exe to dssp, you have to define the executable in your .bashrc file, adding the following line:

alias dssp='/usr/local/bin/dssp.exe'

Then, simply introduce in the command line to apply these changes:

$ source .bashrc

and you're done!

Yes i have done..Thank you all for your valuable suggestions. Thank you Stepphane and Ricardo.

Dear Om could please let me know the steps which you have followed to install DSSP for GROMACS in Linux?

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 ddGeRvDR ddjJlxVr > /dev/null 2> /dev/null

I followed the steps suggested here. But not able to recify. Please help

Dear Jayanthi Jayakumar,

You are getting this error message because dssp is not able to execute the dssp application. Please export you dssp executable before running the do_dssp program.

I am following the above mentioned process only. Initially, i was also getting error like that. Then when i exported my dssp from

export DSSP=/usr/local/bin/dssp/dssp.exe

It was running successfully.

Thanks for the reply Om Sharma.

I tried this export DSSP=/usr/local/bin/dssp/dssp.exe also getting same 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.exe -na ddSewpIG ddjdnopF > /dev/null 2> /dev/null

Please tell me in detail what you have done and how are you doing? I mean from where you taken dssp executible and where you are saving these files and how you are calling the program. Please tell me in detail and step wise, Then only i can find your error step.

Fisrt i got the DSSP exe by giving

sudo wget ftp://ftp.cmbi.ru.ml/pub/software/dssp/dssp-2.0.4-linux-i386 -o /usr/local/bin/dssp

sudo chmod a+x /usr/local/bin/dssp

then checked whether dssp is working or not by giving

/usr/local/bin$ dssp

after that i went to my folder

and gave the command

export DSSP=/usr/local/bin/dssp

After that gave do_dssp command

do_dssp -f til50ns.xtc -s npt.tpr -o ss.xpm

it gave me that 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 ddR0PHpo dd1qwItn > /dev/null 2> /dev/null

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

You need to rename the dssp-2.0.4-linux-i386 file to dssp in the /usr/local/bin folder

Then only you should run the command for do_dssp -f a.xtc -s a.tpr -o a.xpm