[gmx-users] do_dssp

Justin Lemkul jalemkul at vt.edu
Tue Jan 15 13:16:58 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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