[gmx-users] do_dssp

[Justin Lemkul]

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.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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