[gmx-users] DSSP with gmx 5.0.4

[Mark Abraham]

On 03/04/2015 7:36 am, "RJ" <rajiv at kaist.ac.kr> wrote:
>
> Dear gmx users,
>
>
> I tried DSSP of both binary and .exe by renaming it as dssp
(dssp-2.0.4-linux-amd64 & dssp-2.0.4-win32.exe from
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in
usr/local/bin/dssp.

Don't try to install a Windows program. Remove everything and then use only
the Linux version that matches your system.

>
> set the excusable too (  "which dssp" /usr/local/bin/dssp).
>
>
> Both of them gives  same error as follows;
> I also given a permission for dssp file "chmod 777 dssp" but still the
error doesnt go. I use all new version but cant fix it? Any help plz.

That command can only work if you are in the same directory, and as root.
You didn't specify anything about that, so probably the dash binary has the
wrong permissions. Inspect them with ls -l.

Mark

>
> gmx do_dssp -f prd_noPBC.xtc -s prd.tpr -sc scount.xvg -o ss.xpm -dt 10
-ver 2
>
>
> Selected 5: 'MainChain'
> There are 1446 residues in your selected group
> dssp cmd='/usr/local/bin/dssp -i ddiyE5RC -o ddPnxMzu > /dev/null 2>
/dev/null'
> Reading frame       0 time    0.000
> Back Off! I just backed up ddiyE5RC to ./#ddiyE5RC.1#
>
>
> -------------------------------------------------------
> Program gmx, VERSION 5.0.4
> Source code file:
/home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
option.
> -------------------------------------------------------
> Program gmx, VERSION 5.0.4
> Source code file:
/home/raju/gromacs-5.0.4/src/gromacs/gmxana/gmx_do_dssp.c, line: 670
>
>
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver
option.
>
>
>
> --
> 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-request at gromacs.org.