Chiara Parravicini wrote:

Do you refer to pages 58-61 or 148-149 of the manual, about distance restraints and NMR refinement?

Yes. Having read them, and having worked out how to implement them in the context of the tables in section 5.6 4 is prerequisite to you solving your problem :-) "How do I do x?" is not the sort of question to which some random person on the web will give more than a one-sentence answer. This is especially true if the person asking is unknown to them, and hasn't yet demonstrated they've tried all avenues to learn about and/or solve their own problem. See http://www.catb.org/~esr/faqs/smart-questions.html for discussion of such topics :-)

In that case is still not clear to me if the authors in the cited paper use simple distance restraints or apply NMR-derived data, given that the model presented is based on a X-Ray structure.

Nor me. If I had to guess, I'd guess they were just using simple distance restraints. You should be asking the authors, or checking what algorithms are implemented in CHARMM32a216, instead of asking us :-)

So, should I define arbitrary Hbond cutoffs instead of NOE distance restraints?

That depends on the answers to the above, and I've no idea what you mean by "arbitrary Hbond cutoffs" in a GROMACS context.

Mark
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