Ok now after downloading the latest version of dssp, and giving right permissions and after executing the /usr/local/bin/dssp command I am getting the following output :-
[root@BHARATPC peptide2]# /usr/local/bin/dssp DSSP options: -h [ --help ] Display help message -i [ --input ] arg Input file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output -d [ --debug ] arg Debug level (for even more verbose output) Examples: To calculate the secondary structure for the file 1crn.pdb and write the result to a file called 1crn.dssp, you type: dssp.exe -i 1crn.pdb -o 1crn.dssp On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 5/04/2012 5:16 PM, bharat gupta wrote: > > *This is the output : > > [root@BHARATPC ~]# /usr/local/bin/dssp > * > > > Don't run as root except for installing software, unless you like > rebuilding your computer from the ground up. > > *bash: /usr/local/bin/dssp: Permission denied > * > > > Possibly you didn't give execute permission on some file or other. This is > not a GROMACS problem, but rather a problem with how you have done your > dssp installation. Consult its documentation. > > > * > I have already set the pat for dssp in .bashrc using export command , I > don't know why this error is there. Is it due to renaming dsspcmbi to dssp > ?? > * > > > You have now reported testing a command different from the one you > reported that you had instructed do_dssp to use. So it is hard for me to > believe your assertion that you are following the advice in do_dssp -h > correctly with a correct version of DSSP. > > > Mark > > * * > > On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 5/04/2012 4:16 PM, bharat gupta wrote: >> >> Yes , I am using the correct options for dssp. But still I am getting the >> same error. >> >> >> What does invoking /usr/local/bin/dsspcmbi say? >> >> Mark >> >> >> >> On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: >> >>> On 5/04/2012 10:25 AM, bharat gupta wrote: >>> >>>> Hi, >>>> >>>> I am trying to plot the ss content using the do_dssp command , but I am >>>> getting the following error :- >>>> >>>> Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn >>>> ddXN9mH0 > /dev/null 2> /dev/null >>>> >>>> I am using the DSSPold version. What could be the possible reason for >>>> such an error ?? >>>> >>> >>> Many of them. Start by making sure you're following the advice of >>> do_dssp -h. >>> >>> Mark >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> Bharat >> Ph.D. Candidate >> Room No. : 7202A, 2nd Floor >> Biomolecular Engineering Laboratory >> Division of Chemical Engineering and Polymer Science >> Pusan National University >> Busan -609735 >> South Korea >> Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> Mobile no. - 010-5818-3680 >> E-mail : monu46...@yahoo.com >> >> >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists