Re: [gmx-users] dssp error
sometimes it happened if there is any residue that is unknown to DSSP, then it might show this kind of error. I faced it once. On Fri, Mar 22, 2019 at 1:10 AM Mario Andres Rodriguez Pineda < mand...@iq.usp.br> wrote: > I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an > executable > > Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao > escreveu: > > > Have a check the installation of DSSP, > > did you set the variable DSSP for do_dssp? > > > > > > All the best, > > Qinghua > > > > > > On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote: > > > gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm > -tu > > ns > > > -sc cbd211ssp.xvg -ver 2 > > > > > > Program: gmx do_dssp, version 2016.3 > > > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > > > > > > Fatal error: > > > Failed to execute command: Try specifying your dssp version with the > -ver > > > option. > > > > > > > > > Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao < > scorpio.l...@gmail.com > > > > > > escreveu: > > > > > >> Hello, > > >> > > >> Just follow the suggestion by adding "-ver 2" to your command. > > >> > > >> > > >> All the best, > > >> Qinghua > > >> > > >> On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: > > >>> Good afternoon. > > >>> I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP > > 2.0.4 > > >>> for secondary structure analysis. When i try to run it i used this > > >> commad: > > >>> gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns > > -sc > > >>> protssp.xvg > > >>> > > >>> but gromacs send me this error: > > >>> Program: gmx do_dssp, version 2016.3 > > >>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > > >>> > > >>> Fatal error: > > >>> Failed to execute command: Try specifying your dssp version with the > > -ver > > >>> option. > > >>> > > >>> Can you help me to fix this error? > > >>> Thanks for your help > > >>> > > >>> > > >> -- > > >> 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. > > > > -- > *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* > *Estudiante Doctorado en Biotecnología* > > *UNAL- MEDELLÍN/ IQ- USP* > > *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * > *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 > 1475* > -- > 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] dssp error
I downloaded this from dssp ftp page: dssp-2.0.4-linux-amd64, this is an executable Em qui, 21 de mar de 2019 às 16:36, Qinghua Liao escreveu: > Have a check the installation of DSSP, > did you set the variable DSSP for do_dssp? > > > All the best, > Qinghua > > > On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote: > > gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu > ns > > -sc cbd211ssp.xvg -ver 2 > > > > Program: gmx do_dssp, version 2016.3 > > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > > > > Fatal error: > > Failed to execute command: Try specifying your dssp version with the -ver > > option. > > > > > > Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao > > > escreveu: > > > >> Hello, > >> > >> Just follow the suggestion by adding "-ver 2" to your command. > >> > >> > >> All the best, > >> Qinghua > >> > >> On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: > >>> Good afternoon. > >>> I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP > 2.0.4 > >>> for secondary structure analysis. When i try to run it i used this > >> commad: > >>> gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns > -sc > >>> protssp.xvg > >>> > >>> but gromacs send me this error: > >>> Program: gmx do_dssp, version 2016.3 > >>> Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > >>> > >>> Fatal error: > >>> Failed to execute command: Try specifying your dssp version with the > -ver > >>> option. > >>> > >>> Can you help me to fix this error? > >>> Thanks for your help > >>> > >>> > >> -- > >> 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. -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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] dssp error
Have a check the installation of DSSP, did you set the variable DSSP for do_dssp? All the best, Qinghua On 3/21/19 8:01 PM, Mario Andres Rodriguez Pineda wrote: gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao escreveu: Hello, Just follow the suggestion by adding "-ver 2" to your command. All the best, Qinghua On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Can you help me to fix this error? Thanks for your help -- 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] dssp error
gmx do_dssp -f cbd211_mdnopbc.xtc -s cbd211_md.tpr -o cbd211_ssp.xpm -tu ns -sc cbd211ssp.xvg -ver 2 Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Em qui, 21 de mar de 2019 às 15:53, Qinghua Liao escreveu: > Hello, > > Just follow the suggestion by adding "-ver 2" to your command. > > > All the best, > Qinghua > > On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: > > Good afternoon. > > I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 > > for secondary structure analysis. When i try to run it i used this > commad: > > > > gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc > > protssp.xvg > > > > but gromacs send me this error: > > Program: gmx do_dssp, version 2016.3 > > Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) > > > > Fatal error: > > Failed to execute command: Try specifying your dssp version with the -ver > > option. > > > > Can you help me to fix this error? > > Thanks for your help > > > > > > -- > 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. > -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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] dssp error
Hello, Just follow the suggestion by adding "-ver 2" to your command. All the best, Qinghua On 3/21/19 7:50 PM, Mario Andres Rodriguez Pineda wrote: Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Can you help me to fix this error? Thanks for your help -- 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] dssp error
Good afternoon. I'm using Gromacs 2016 to do a dynamic simulation. I installed DSSP 2.0.4 for secondary structure analysis. When i try to run it i used this commad: gmx do_dssp -f prot_mdnopbc.xtc -s prot_md.tpr -o prot_ssp.xpm -tu ns -sc protssp.xvg but gromacs send me this error: Program: gmx do_dssp, version 2016.3 Source file: src/gromacs/gmxana/gmx_do_dssp.cpp (line 668) Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. Can you help me to fix this error? Thanks for your help -- *MSc. MARIO ANDRÉS RODRÍGUEZ PINEDA* *Estudiante Doctorado en Biotecnología* *UNAL- MEDELLÍN/ IQ- USP* *Grupo de Pesquisa em Ressonância Magnética Nuclear de Biomoléculas * *Av. Prof. Lineu Prestes 748, Sao Paulo SP, 05508-000, Tel: + 55 11 3091 1475* -- 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] DSSP Error
Hi to all first i run 'gmx do_dssp -s md.tpr -f md.xtc' i go this error: Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) then i put dssp executable file in the path 'usr/local/bin/dssp' and run following command : 'export DSSP=/usr/local/bin/dssp' now when i run gmx do_dssp i get this error: 'Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option.' even with use of-ver option, i got the same error. what can i do to solve this problem? thanks for your help -- 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.