[gmx-users] Noe distance restraints

[Mark Abraham]

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