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<p style="margin-bottom: 0cm;">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.</p>
<p style="margin-bottom: 0cm;">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.
</p>
<p style="margin-bottom: 0cm;">
Thank you very much for your patience and your advices.</p>
<p style="margin-bottom: 0cm;">Chiara</p>
<br><br><div class="gmail_quote">On Fri, Feb 29, 2008 at 2:04 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">Chiara Parravicini wrote:<br>
><br>
> Do you refer to pages 58-61 or 148-149 of the manual, about distance<br>
> restraints and NMR refinement?<br>
<br>
</div>Yes. Having read them, and having worked out how to implement them in<br>
the context of the tables in section 5.6 4 is prerequisite to you<br>
solving your problem :-) "How do I do x?" is not the sort of question to<br>
which some random person on the web will give more than a one-sentence<br>
answer. This is especially true if the person asking is unknown to them,<br>
and hasn't yet demonstrated they've tried all avenues to learn about<br>
and/or solve their own problem. See<br>
<a href="http://www.catb.org/%7Eesr/faqs/smart-questions.html" target="_blank">http://www.catb.org/~esr/faqs/smart-questions.html</a> for discussion of<br>
such topics :-)<br>
<div class="Ih2E3d"><br>
> In that case is still not clear to me if the authors in the cited paper<br>
> use simple distance restraints or apply NMR-derived data, given that the<br>
> model presented is based on a X-Ray structure.<br>
<br>
</div>Nor me. If I had to guess, I'd guess they were just using simple<br>
distance restraints. You should be asking the authors, or checking what<br>
algorithms are implemented in CHARMM32a216, instead of asking us :-)<br>
<div class="Ih2E3d"><br>
> So, should I define arbitrary Hbond cutoffs instead of NOE distance<br>
> restraints?<br>
<br>
</div>That depends on the answers to the above, and I've no idea what you mean<br>
by "arbitrary Hbond cutoffs" in a GROMACS context.<br>
<div><div></div><div class="Wj3C7c"><br>
Mark<br>
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