[gmx-users] do_dssp

[Justin Lemkul]

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

-- 
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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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