You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/ It is also in the ubuntu repo. You should to get mkdssp and/or dssp to work on their own and if you can't then your problem is not with gmx.
On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu <simoncks1...@gmail.com > wrote: > Hi everyone, > > I linked dssp as mkdssp and it still does not work. I try to run dssp in > terminal. This is the result. > > mkdssp 2.2.1 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 > --version Print version > -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 -i 1crn.pdb -o 1crn.dssp > > Hope it behaves normally. > > Simon > > 2018-03-13 17:07 GMT+08:00 Mark Abraham <mark.j.abra...@gmail.com>: > > > Hi, > > > > gmx do_dssp -h > > > > says everything there is to say about how to get this to work. I've no > idea > > what mkdssp is, but unless it does the same things as dssp, it won't > work. > > > > Mark > > > > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu < > simoncks1...@gmail.com > > > > > wrote: > > > > > Hi João, > > > > > > Thanks for your suggestion. Unfortunately, the error persists. I > thought > > > -ver 2 was the default value. > > > > > > Regards, > > > Simon > > > > > > 2018-03-13 15:58 GMT+08:00 João Henriques < > joao.m.a.henriq...@gmail.com> > > : > > > > > > > "Fatal error: Failed to execute command: Try specifying your dssp > > version > > > > with the -ver option." > > > > > > > > Did you follow the error message suggestion? With DSSP 2.2.1 you need > > to > > > > set "-ver 2" on your gmx do_dssp command. > > > > > > > > J > > > > > > > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu < > > > > simoncks1...@gmail.com> > > > > wrote: > > > > > > > > > Hi everyone. > > > > > > > > > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It > > > returned > > > > > an error: > > > > > > > > > > > > > > > Fatal error: > > > > > Failed to execute command: Try specifying your dssp version with > the > > > -ver > > > > > option. > > > > > > > > > > > > > > > I can run mkdssp and it is placed in bin. Is it a compatibility > > problem > > > > > here? > > > > > > > > > > Thanks in advance. > > > > > > > > > > Regards. > > > > > Simon > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at http://www.gromacs.org/ > > > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at http://www.gromacs.org/ > > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Joe Jordan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.