[gmx-users] gmx do_dssp

Eduardo Diniz dududiniz94 at hotmail.com
Mon Mar 18 17:44:52 CET 2019


I'm wanting to keep track of secondary structure (ss) elements in my protein simulation but I have some questions about the do_dssp tool of gromacs. The two main output files it produces is a ss.xpm file which I've found very difficult to interpret, mainly because I don't know what that colors code represent and the x and y axis are not specified (I think the x axis is time and the y axis is residue).

The second file is the scount.xvg file which indicates the number of residues belonging to one of eight secondary structure elements, but for me this information isn't enough, because I want to know what residues belong to what ss element.

One optinal output file that I think might be useful for me is the ssdump.dat file, which shows (I suppose) what residues belongs to what ss elements, but I don't know what those letters (E, S H etc) means.

Sorry if what I ask is stupid. Hope someone can help me. Thanks in advance for your time.


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