[gmx-users] Regarding DSSP

HANNIBAL LECTER hanniballecter13 at gmail.com
Mon Feb 16 21:15:26 CET 2015

Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not
a scope to specify using the -ver command in this particular version as
opposed to the newer versions (5.0.4).

By '....' I meant

do_dssp -f prot.xtc -s prot.tpr.

How do I specify a dssp version in gromacs-4.5.6?

Secondly, I did install Gromacs-5.0.4 for comparison, and I am using DSSP
2.0.4 again. This time I am using

do_dssp -f prot.xtc -s prot.tpr -ver 2

The output I am getting is shown below. Not sure what is going on.

*There are 18 residues in your selected groupdssp cmd='/usr/bin/mkdssp -i
ddJszHtZ -o ddRZ5pwg > /dev/null 2> /dev/null'Reading frame       0 time
0.000   Back Off! I just backed up ddJszHtZ to
do_dssp, VERSION 5.0.4Source code file:
line: 670Fatal error:Failed to execute command: Try specifying your dssp
version with the -ver option.For more information and tips for
troubleshooting, please check the GROMACSwebsite at

More information about the gromacs.org_gmx-users mailing list