[gmx-users] Using do_dssp with GROMACS 4.6.7.

[Justin Lemkul]

On 1/29/15 9:16 PM, Agnivo Gosai 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.
>

Given that all of your invocations of do_dssp fail, it means something 
fundamental is wrong.  Your environment variable is set incorrectly.  Don't 
point to the directory containing the binary, point the binary itself.  From the 
help description:

"If this is not the case, then you should set an environment variable DSSP 
pointing to the dssp executable"

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================