[gmx-users] Noe distance restraints

[Chiara Parravicini]

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
done.

Thank you very much for your patience and your advices.

Chiara


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

> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080229/956186e9/attachment.html>