[gmx-users] Re: Re: do_dssp for many peptides

[Justin Lemkul]

> do_dssp claims that are 248 residues in my selected group, although 248
> is the number of *atoms* (not of residues) of this peptide. After the
> notion that some temporary file is backed up, do_dssp gets stuck again.
>
> I have even tried exactly Mark's suggestion (xtc file containing single
> peptide) for test reasons, but a similar problem occurs for the peptide
> denoted as chain N: do_dssp claims that are 124 residues in my selected
> group, although 124 is the number of *atoms* (not of residues) of this
> peptide. After the notion that some temporary file is backed up, do_dssp
> gets stuck again.

I saw a similar description in the archives a long time ago when I was looking
for help on do_dssp and experiencing similar problems (with a simpler system,
granted).  Which group are you selecting for running do_dssp?  These errors
seem to come up if you select any group other than 'MainChain' (choice 5, I
believe).  If do_dssp is finding an incorrect number of "residues," perhaps you
have selected 'Protein' instead of 'MainChain' for your analysis?

-Justin


Justin A. Lemkul
Department of Biochemistry
Virginia Tech