[gmx-users] do_dssp

Justin Lemkul jalemkul at vt.edu
Tue Dec 17 08:44:21 CET 2019



On 12/16/19 12:21 PM, Iman Katouzian wrote:
> Good day,
>
> I am using do_dssp to determine the secondary structure of my protein
> however when I run my code :
> gmx do_dssp -f final.xtc -s md.tpr -n index.ndx -o ss.xpm -sc scount.xvg
> -tu ns
> I encounter this, and after several minutes the reading time frames is
> still ZERO!!
> I have already did chmod +x dssp in  ----> '/usr/local/bin/dssp
>
> *Here is the message after running the code:*
>   -i ddub26pK 2>/dev/null'
> Reading frame       0 time    0.000
> Back Off! I just backed up ddub26pK to ./#ddub26pK.1#
>

The command is slow and won't update with every frame it reads.

-Justin

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Justin A. Lemkul, Ph.D.
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