[gmx-users] do_dssp for fragment

[Anton Feenstra]

Mateusz Nowak wrote:
> 
> 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?

The fragment will be analyzed as if it was a completely isolated
molecule,
so no interaction with other parts of the protein will be included.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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