[gmx-users] do_dssp for many peptides

Volker Knecht vknecht at mpikg.mpg.de
Wed May 23 11:43:00 CEST 2007

Dear all,

I have a problem with applying do_dssp to a system containing 24 
peptides with 15 residues and 124 atoms per peptide (solvent removed, 

I observe the following behavior:

(1) When I try to apply dssp to all peptides, do_dssp says "There are 
1668 residues in your selected group" (although there are only  360 
residues), and the eps version of the output ss.xpm (ss.eps) is just black.

(2) If I restrict the analysis to a peptide denoted as chain J, dssp 
replies correctly that there are 15 residues in the selected group, and 
the ss.eps produced looks fine.

(3) If I perform the analysis on a peptide denoted as chain N, dssp 
claims that are 124 residues in my selected group. But, in fact, 124 is 
the number of atoms of this peptide as noted above. After the notion 
that some temporary file is backed up, do_dssp seems to get stuck.

I suspect the following: Note that 1668 = 12*15 + 12*124. It seems that 
exactly half of the peptides are recognized properly (15 residues per  
peptide), while the others are not recognized properly as noted above 
(124 residues per peptide). I guess it is the first half (chains A-L) 
that is treated fine, while the second half (chains M-X) produces a 
flawed behavior of do_dssp.

Does anyone have an idea what is going wrong?


Dr. Volker Knecht
Department of Theory and Bio-Systems
Max Planck Institute of Colloids and Interfaces
Research Campus Golm
14424 Potsdam, Germany

Phone: +49-331-567-9610
Fax: +49-331-567-9612

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