[gmx-users] dssp on results of HREX simulation

Shyno Mathew sm3334 at columbia.edu
Sun Oct 4 02:52:36 CEST 2015


Dear all,


*I was able to fix the error mentioned in the previous message. Here is
what I did:*

wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
/vega/cheme/users/sm3334/DSSP/dssp


chmod a+x /vega/cheme/users/sm3334/DSSP/dssp

Modify the .bashrc file
export DSSP=/vega/cheme/users/sm3334/DSSP/dssp

*Now I have a question regarding the secondary structure plot. *
How can I make sure the plots shows the maximum x value, y value completely?

Please view the plot here:

https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing



Following are the contents of the .m2p file:
black&white              = no           ; Obsolete
titlefont                = Times-Roman  ; A PostScript Font
titlefontsize            = 300          ; Font size (pt)
legend                   = yes          ; Show the legend
legendfont               = Times-Roman  ; A PostScript Font
legendfontsize           = 250          ; Font size (pt)
xbox                     = 1.0          ; x-size of a matrix element
ybox                     = 20.0         ; y-size of a matrix element
matrixspacing            = 30.0         ; Space between 2 matrices
xoffset                  = 0.0          ; Between matrix and bounding box
yoffset                  = 0.0          ; Between matrix and bounding box
x-major                  = 1000         ; Major ticks on x axis every ..
frames
x-minor                  = 500          ; Id. Minor ticks
x-firstmajor             = 5000         ; First frame for major tick
x-majorat0               = no           ; Major tick at first frame
x-majorticklen           = 40.0          ; x-majorticklength
x-minorticklen           = 20.0          ; x-minorticklength
x-label                  =              ; Used when there is none in the
.xpm
x-fontsize               = 250          ; Font size (pt)
x-font                   = Times-Roman  ; A PostScript Font
x-tickfontsize           = 200          ; Font size (pt)
x-tickfont               = Helvetica    ; A PostScript Font
y-major                  = 20
y-minor                  = 10
y-firstmajor             = 0
y-majorat0               = no
y-majorticklen           = 40.0
y-minorticklen           = 20.0
y-label                  =
y-fontsize               = 250
y-font                   = Times-Roman
y-tickfontsize           = 200
y-tickfont               = Helvetica

thanks,

Shyno



On Sat, Oct 3, 2015 at 8:48 PM, Shyno Mathew <sm3334 at columbia.edu> wrote:

> Dear all,
>
>
> wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O
> /vega/cheme/users/sm3334/DSSP/dssp
>
> chmod a+x /vega/cheme/users/sm3334/DSSP/dssp
>
> Modify the .bashrc file
> export DSSP=/vega/cheme/users/sm3334/DSSP/dssp
>
> *Now I have a question regarding the secondary structure plot. *
> How can I make sure the plots shows the maximum x value, y value
> completely?
> Please view the plot here:
>
> https://drive.google.com/file/d/0B-CUIoblZxdlV3JFdTZFQlJUYnc/view?usp=sharing
>
>
> Following are the contents of the .m2p file:
> black&white              = no           ; Obsolete
> titlefont                = Times-Roman  ; A PostScript Font
> titlefontsize            = 300          ; Font size (pt)
> legend                   = yes          ; Show the legend
> legendfont               = Times-Roman  ; A PostScript Font
> legendfontsize           = 250          ; Font size (pt)
> xbox                     = 1.0          ; x-size of a matrix element
> ybox                     = 20.0         ; y-size of a matrix element
> matrixspacing            = 30.0         ; Space between 2 matrices
> xoffset                  = 0.0          ; Between matrix and bounding box
> yoffset                  = 0.0          ; Between matrix and bounding box
> x-major                  = 1000         ; Major ticks on x axis every ..
> frames
> x-minor                  = 500          ; Id. Minor ticks
> x-firstmajor             = 5000         ; First frame for major tick
> x-majorat0               = no           ; Major tick at first frame
> x-majorticklen           = 40.0          ; x-majorticklength
> x-minorticklen           = 20.0          ; x-minorticklength
> x-label                  =              ; Used when there is none in the
> .xpm
> x-fontsize               = 250          ; Font size (pt)
> x-font                   = Times-Roman  ; A PostScript Font
> x-tickfontsize           = 200          ; Font size (pt)
> x-tickfont               = Helvetica    ; A PostScript Font
> y-major                  = 20
> y-minor                  = 10
> y-firstmajor             = 0
> y-majorat0               = no
> y-majorticklen           = 40.0
> y-minorticklen           = 20.0
> y-label                  =
> y-fontsize               = 250
> y-font                   = Times-Roman
> y-tickfontsize           = 200
> y-tickfont               = Helvetica
>
> thanks,
> Shyno
>
> On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew <sm3334 at columbia.edu> wrote:
>
>> Dear all,
>>
>> I am getting errors while using do_dssp. I am able to select the main
>> chain for analysis.
>>
>> Following is the error I am getting:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *There are 120 residues in your selected groupdssp
>> cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
>> /dev/null'Reading frame       0 time 5000.000   Back Off! I just backed up
>> dd7XLZVM to
>> ./#dd7XLZVM.1#-------------------------------------------------------Program
>> do_dssp_mpi, VERSION 4.6.7Source code file:
>> /vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
>> line: 669Fatal error:Failed to execute command: Try specifying your dssp
>> version with the -ver option.*
>>
>>
>> Here is the location of DSSP:
>> /vega/cheme/users/sm3334/DSSP
>>
>> As mentioned in the gromacs website/mailing list, I included the path in
>> the .bashrc file
>> I tried all the following options, but I am still getting error:
>>
>> export DSSP=/vega/cheme/users/sm3334/DSSP
>> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs
>> -4.6.7/src/tools/do_dssp.c
>> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
>> DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
>>
>> Sincerely,
>> Shyno
>>
>> --
>> Shyno Mathew
>> PhD Candidate
>> Department of Chemical Engineering
>> Graduate Assistant
>> Office of Graduate Student Affairs
>> The Fu Foundation School Of Engineering and Applied Science
>> Columbia University
>>
>
>
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>
> On Sat, Oct 3, 2015 at 1:56 PM, Shyno Mathew <sm3334 at columbia.edu> wrote:
>
>> Dear all,
>>
>> I am getting errors while using do_dssp. I am able to select the main
>> chain for analysis.
>>
>> Following is the error I am getting:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *There are 120 residues in your selected groupdssp
>> cmd='/vega/cheme/users/sm3334/DSSP -i dd7XLZVM -o ddkpNsfY > /dev/null 2>
>> /dev/null'Reading frame       0 time 5000.000   Back Off! I just backed up
>> dd7XLZVM to
>> ./#dd7XLZVM.1#-------------------------------------------------------Program
>> do_dssp_mpi, VERSION 4.6.7Source code file:
>> /vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs-4.6.7/src/tools/gmx_do_dssp.c,
>> line: 669Fatal error:Failed to execute command: Try specifying your dssp
>> version with the -ver option.*
>>
>>
>> Here is the location of DSSP:
>> /vega/cheme/users/sm3334/DSSP
>>
>> As mentioned in the gromacs website/mailing list, I included the path in
>> the .bashrc file
>> I tried all the following options, but I am still getting error:
>>
>> export DSSP=/vega/cheme/users/sm3334/DSSP
>> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/gromacs
>> -4.6.7/src/tools/do_dssp.c
>> export DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
>> DSSP=/vega/cheme/users/sm3334/GROMACSwPLUMED/bin/do_dssp_mpi
>>
>> Sincerely,
>> Shyno
>>
>> --
>> Shyno Mathew
>> PhD Candidate
>> Department of Chemical Engineering
>> Graduate Assistant
>> Office of Graduate Student Affairs
>> The Fu Foundation School Of Engineering and Applied Science
>> Columbia University
>>
>
>
>
> --
> Shyno Mathew
> PhD Candidate
> Department of Chemical Engineering
> Graduate Assistant
> Office of Graduate Student Affairs
> The Fu Foundation School Of Engineering and Applied Science
> Columbia University
>



-- 
Shyno Mathew
PhD Candidate
Department of Chemical Engineering
Graduate Assistant
Office of Graduate Student Affairs
The Fu Foundation School Of Engineering and Applied Science
Columbia University


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