[gmx-users] do_dssp

[Miguel Ángel Mompeán García]

I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:

dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
/dev/null'
Reading frame       0 time    0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#

-------------------------------------------------------
Program do_dssp, VERSION 4.6
Source code file: /usr/local/bin/gromacs-4.6/src/tools/gmx_do_dssp.c, line:
667

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.

How can I fix that?

Thanks







2013/1/15 James Starlight <jmsstarlight at gmail.com>

> Justin, thanks both options works perfect.
>
>
> James
>
> 2013/1/15 Justin Lemkul <jalemkul at vt.edu>:
> >
> >
> > On 1/15/13 7:13 AM, James Starlight wrote:
> >>
> >> Justin,
> >>
> >>
> >>   I  want to obtain timescale on X as well as number of residues on Y
> >> on the xmp graph . By  default that graph has not legend so it's hard
> >> to analyse it .
> >>
> >
> > The legends are printed in the .xvg header.  I've never had a problem
> > plotting its contents (though they are usually somewhat unclear when
> plotted
> > together) with xmgrace -nxy scount.xvg
> >
> >
> >> By the way have you forced with some problems with dppc ? Simetimes
> >> I've obtain error like
> >>
> >>
> >> There are 286 residues in your selected group
> >> dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 > /dev/null 2>
> >> /dev/null'
> >> Reading frame       0 time    0.000
> >> Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1
> >>
> >>
> >> Fatal error:
> >> Failed to execute command: Try specifying your dssp version with the
> >> -ver option.
> >>
> >> and I dont know how to fix it.
> >>
> >> I'm using gromacs-4.6-beta 3 with dssp 2.0.3
> >>
> >
> > Since dssp changed its command line options, Gromacs had to adapt as
> well.
> > The error tells you to use the -ver option; you should do so.  Version 2
> > should be the default, so check to make sure you're actually using that
> > version and not the old dssp.
> >
> >
> > -Justin
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
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