[gmx-users] dssp doubt

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 7 16:10:55 CEST 2012

On 6/7/12 10:07 AM, Turgay Cakmak wrote:
> Hi all,
> I downloaded the original form of DSSP which is recently called
> DSSPold. Whenever I use the following:
> *do_dssp -s  topol.tpr  -f  t raj.xtc  -o  ss.xpm *
> It selects "Protein" by it-self without any control from me. I want to choose
> from the list, for example not protein but C-alpha.

That shouldn't happen.  You should be prompted for a selection.  Note that 
selecting only C-alpha atoms will not work.  DSSP requires all MainChain atoms 
to be considered, since the secondary structure criteria are based on hydrogen 
bonding distances.  An incorrect selection could explain the error you get below.


> To solve this probIem, I prepared the index file which includes only C-alphas of
> my system. Then, I use the following:
> *do_dssp  -s  topol.tpr  -f   traj.xtc  -n   C_alpha.ndx*
>   I get the below fatal error:
> Program do_dssp, VERSION 4.5.4
> Source code file: do_dssp.c, line: 566
> Fatal error:
> Failed to execute command: /home_palamut2/mguler/dssp/dsspcmbi -na ddcblxTU
> ddq8aNVV > /dev/null 2> /dev/null
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Are there any suggestions or corrections? Thanks in advance..
> Turgay


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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