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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