[gmx-users] do_dssp for fragment

[Mateusz Nowak]

Hi gmx-users!

Since the recognition of secondary structure by DSSP algorithm is based on
H bond network, I was wondering what happens if I analyze only the part of
my protein using do_dssp. Will H bonds between specicied fragment and the
rest of the protein be taken into account? Or rather only H bonds created
inside fragment specicied in index file?

Thanks in advence!

Mateusz Nowak