[gmx-users] DSSP

[Justin Lemkul]

On 3/21/17 5:13 AM, Aishwarya Dhar wrote:
> Following procedure I have used
> 1. Downloaded  http://swift.cmbi.ru.nl/gv/dssp/
> dssp-2.0.4-linux-i386 and renamed it dssp
>
> 2.made dssp  executable  and moved it to usr/local/bin
>
> 3.Then ran the command from the current location where the tpr and trr
> files are present do_dssp -s  md.tpr -f md.trr -o ss.xpm  -ver 2.0
>
> 4.There are 91 residues in your selected group dssp cmd='/usr/local/bin/dssp
> -i ddixopnV -o dd4YitS9 > /dev/null 2> /dev/null'
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time    0.000
> Back Off! I just backed up ddixopnV to ./#ddixopnV.1#
>
> It seems that the run is going on for two weeks and dssp analysis couldnt
> be done
>

How many frames did you save?  do_dssp is a very slow program (it's just a 
wrapper to call dssp) and if you have tons of frames, it will take a long time. 
You can always list the files in the directory in which do_dssp is operating and 
you should see temporary files prefixed with "dd" being created and over-written.

You can always test whether or not do_dssp is working by passing it a single 
frame to -f, rather than waiting for a very expensive .trr file to be processed 
in full.

-Justin

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> Thanks
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> Sincerely
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> Aishwarya Dhar
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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