[gmx-users] do-dssp

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 7 20:03:44 CET 2008

David Mobley wrote:
> 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?
Yes. The way to check this is to run normal dssp on a pdb file and 
insect the output.
> Thanks,
> David
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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