[gmx-users] do_dssp for many peptides
vknecht at mpikg.mpg.de
Wed May 23 11:43:00 CEST 2007
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
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