[gmx-users] Ramachandran Plot

[Anton Feenstra]

David wrote:
> If you have a stable structure with wrong angles, there maybe something
> fishy. If it just happens a short time during your 10 ns, don't worry...
> (but do check it!)

If I may add, the different regions in the ramachandram typed
as 'favored', 'allowed' and 'disallowed' are derived from *protein*
structures and may not be applicable to a peptide, that could be
much more flexible even at a few ns timescale than a protein ever
could.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|