[gmx-users] do-dssp

[David Mobley]

All,

I'm using do_dssp to do some secondary structure analysis. I have a
peptide with two nonstandard residues, one at the N-terminus and one
at the C-terminus, and a total of N residues. The output of do_dssp
only contains information on N-2 residues (numbered 1 through N-2)
while my trajectory input contains information on the full N residues.
I'm guessing this is because dssp doesn't know how to calculate
secondary structure for nonstandard residues, and so it simply omits
the two nonstandard residues and then numbers the remaining residues
consecutively beginning at 1. Is this correct?

Thanks,
David