normal create sekundär struktur and limitation when not

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4 months 2 weeks ago #7760 by Newguy
Newguy created the topic: create sekundär struktur and limitation when not
Moin everybody :D

This question would be a little bit between the topics.

For the moment I am having a problem with the definition of the secondary structure of a 10 AS long peptide. (something new)
The working group would like it to be beta-string extended (do not know how to do it in martinize. The explizit creation with Amber xleap and the command -p backbone in martinize seems to work somehow butttttt.....
Sometimes it forms rings.....)

How do I create this secondary structure?

So the secondary structure seems to be not correct (but my professor would really like it to be more flexible and said nice!!!)

Yeah.... that is not correct any more or?
In the review it said every secondary structure needs to be given
(my data would be bul§$shi"§$ or?)

Thanks for your thoughts and expertize :)

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4 months 2 weeks ago #7761 by Newguy
Newguy replied the topic: create sekundär struktur and limitation when not
didn't know if the limitation part would be in the philosophy. Kinds of connect to martinize.py but the limitation part seemed to be more important.

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4 months 2 weeks ago #7762 by peterkroon
peterkroon replied the topic: create sekundär struktur and limitation when not
Hi!

In general, Martini proteins (and peptides) can not change secondary structure, since the different structure elements have different parameters.

As for Martinize, you can give an secondary structure as a string with the `-ss` option. An extended beta-sheet is probably described as 'E', so just feed `-ss EEEEEEEEEE...` (with the same number of E's as amino acids) to martinize.
Usually these secondary structures are also enforced using an elastic network, but depending on how large your peptide is this may not be too usefull. Experiment with the `-ed` flag.

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4 months 2 weeks ago #7763 by Newguy
Newguy replied the topic: create sekundär struktur and limitation when not
thanks going to try that :D

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