[gmx-users] dssp doubt

Turgay Cakmak turgaycakmak34 at gmail.com
Thu Jun 7 16:07:00 CEST 2012

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.

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..

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120607/0de7cd06/attachment.html>

More information about the gromacs.org_gmx-users mailing list