[gmx-users] Using do_dssp with GROMACS 4.6.7.

[Agnivo Gosai]

Hello

I am sorry for wasting your time. The online GROMACS help is enough to fix
my problem.

I am giving it below.

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

The problem is fixed now!!

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

On Thu, Jan 29, 2015 at 8:16 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Dear Users
>
> I want to calculate the secondary structure stability by using DSSP in
> GROMACS 4.6.7.
> These are the commands that I used for the same :-
>
> (1) ./dssp-2.0.4-linux-i386  ( I am running the DSSP executable )
>
> (2) source /usr/local/gromacs/bin/GMXRC (sourcing GROMACS from my terminal)
>
> (3) export DSSP=/home/upamanyu/Desktop/GROMACS (exporting the path to the
> DSSP executable , it is located tin the folder GROMACS)
>
>  (4) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 2
>
> I am able to select the group protein at this stage. Then on hitting enter
> this error comes.
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
> option.
>
>
>  (5) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 1
>
> Same error comes
>
>  (6)  do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc
>
> Same error comes
>
>  (7) do_dssp_467 -s pull1.tpr -f pull1_noPBC.xtc -ver 2.0.4
>
> Same error comes
>
>  (8)  ./dssp-2.0.4-linux-i386 -i pull1.pdb -o pull1.dssp
>
> This works fine. But I want to use GROMACS to generate plots and figures
> with its do_dssp command.
>
> Kindly help me to find a solution.
>
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
>