[gmx-users] Noe distance restraints

Chiara Parravicini parravicini.chiara at gmail.com
Fri Feb 29 15:09:24 CET 2008

I surely searched for answers looking through gromacs, charmm documentation,
mailing list, web, literature, etc. before posting my question. I know that
it sounds inappropriate because it isn't a technical question, nevertheless
I still wasn't able to solve the apparent contradiction between NMR data and
X-ray structures. So I thought that I had missed some technical detail to do
that with gromacs and I then asked to the mailing list.

Anyway, with "arbitrary Hbond cutoffs" I mean simple distance restraints
with a Hbond length. Maybe, as you suggested in the cited papers the same is

Thank you very much for your patience and your advices.


On Fri, Feb 29, 2008 at 2:04 PM, Mark Abraham <Mark.Abraham at anu.edu.au>

> 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<http://www.catb.org/%7Eesr/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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