[gmx-users] DSSP installation on Ubuntu 12.10

[Mark Abraham]

Hi,

Since the release of 4.5.5, DSSP totally changed its command-line
interface. So old GROMACS code cannot work with new DSSP. You need to get
the old version of DSSP to use with old GROMACS, or new GROMACS code to
work with either DSSP.

Mark


On Thu, Oct 10, 2013 at 1:37 PM, Mass <masstransfer_2010 at yahoo.com> wrote:

> Dear Gromacs users,
> I have asked this questions before and Justin gave some answers which I
> could solve my problem based on his answer. I am using Ubuntu 12.10 and
> installed gromacs 4.5.5-2.
> this is what I have done
> 2- I moved this file to usr/local/bin
> 1- first I downloaded the dssp
> wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64-O~/dssp
> 2- I moved this file to usr/local/bin
>
> then I run do_dssp  and I was asked to select a group
> Select a group: 1
> Selected 1: 'Protein'
> There are 162 residues in your selected group
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time    0.000
> Back Off! I just backed up ddQ0FCUF to ./#ddQ0FCUF.1#
>
> after that I am getting
> Program do_dssp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line:
> 572
>
> Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddQ0FCUF ddzUlAvc >
> /dev/null 2> /dev/null
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I really appreciate if anyone can tell me simple and step-by step solution
> (I am a beginner user).
>
> Thanks
>
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