Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
Ok, there's quite a lot going on here. The mkdssp the OP talks about is the default name for the executable you get upon compilation from source. Naming it dssp makes more sense, so that's why I suggested making a link called dssp. Either way, it shouldn't matter because if you give the right path to mkdssp or dssp or whatever name you give it, it should work. If the standalone execution of dssp works, the problem must be with the export. Please confirm that you have exported the DSSP environment variable correctly. Type "$DSSP -h" for example. If that works, then there's no reason for gmx do_dssp to not work. P.S.: dssp is notoriously tricky to compile, e.g. the static flag issue. I also recently noticed that with boost >= 1.65.1, the code gets seriously broken and needs some major modifications (see https://pastebin.com/NiQJkjuC ). J On Tue, Mar 13, 2018 at 10:30 AM, Simon Kit Sang Chu wrote: > Thank you, Joe. I re-ensure that dssp works in my case. I tried: > > dssp prod-protein.pdb -o test.dssp > > The result looks fine without error text. > > Simon > > 2018-03-13 17:24 GMT+08:00 Joe Jordan : > > > 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 ] argInput file > > > -o [ --output ] arg Output file, use 'stdout' to output to screen > > > -v [ --verbose ] Verbose output > > > --version Print version > > > -d [ --debug ] argDebug 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 : > > > > > > > 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.
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
I had a similar issue with dssp which suddenly stopped working. Switching to x86 binary worked for me. Linux Arch Mat On Tue, 13 Mar 2018, 09:25 Joe Jordan, wrote: > 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 ] argInput file > > -o [ --output ] arg Output file, use 'stdout' to output to screen > > -v [ --verbose ] Verbose output > > --version Print version > > -d [ --debug ] argDebug 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 : > > > > > 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 requ
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
Thank you, Joe. I re-ensure that dssp works in my case. I tried: dssp prod-protein.pdb -o test.dssp The result looks fine without error text. Simon 2018-03-13 17:24 GMT+08:00 Joe Jordan : > 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 ] argInput file > > -o [ --output ] arg Output file, use 'stdout' to output to screen > > -v [ --verbose ] Verbose output > > --version Print version > > -d [ --debug ] argDebug 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 : > > > > > 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 > > > >
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
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 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 ] argInput file > -o [ --output ] arg Output file, use 'stdout' to output to screen > -v [ --verbose ] Verbose output > --version Print version > -d [ --debug ] argDebug 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 : > > > 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.
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
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 ] argInput file -o [ --output ] arg Output file, use 'stdout' to output to screen -v [ --verbose ] Verbose output --version Print version -d [ --debug ] argDebug 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 : > 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 > > 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 > : > > > > > "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.
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
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 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 : > > > "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.
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
Is the export consistent with the executable name? J On Tue, Mar 13, 2018 at 9:55 AM, Simon Kit Sang Chu 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 : > > > "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.
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
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 : > "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.
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
Also, if you're exporting DSSP="/.../dssp" and your bin contains mkdssp and not dssp, then that's going to fail for obvious reasons. Either export DSSP="/.../mkdssp" or create a link to mkdssp within the same directory with the name "dssp" (ln -s mkdssp dssp). Export and executable name must match. J On Tue, Mar 13, 2018 at 8:58 AM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > "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.
Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1
"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 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.
[gmx-users] GROMACS 5.1.4 and dssp 2.2.1
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.
