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-</style>Do you refer to pages 58-61 or 148-149
of the manual, about distance restraints and NMR refinement?
<p style="margin-bottom: 0cm;">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.
</p>
<p style="margin-bottom: 0cm;">So, should I define arbitrary Hbond
cutoffs instead of NOE distance restraints?</p>
<p style="margin-bottom: 0cm;">Sorry for being insistent but I cannot
come through the question.<br></p>
<p style="margin-bottom: 0cm;">
</p>
<p style="margin-bottom: 0cm;">Thanks in advance
</p>
<p style="margin-bottom: 0cm;">
</p>
<p style="margin-bottom: 0cm;">Chiara</p>
<br><div class="gmail_quote">On Fri, Feb 29, 2008 at 11:08 AM, 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><div></div><div class="Wj3C7c">> Dear Gromacs users,<br>
><br>
> I'd like to perform a simulation following the protocol applied in the<br>
> Ivanov's paper (*Molecular dynamics simulation of the P2Y14 receptor.<br>
> Ligand<br>
> docking and identification of a putative binding site of the distal hexose<br>
> moiety.* *Bioorg. Med Chem Lett.* 2007;17(3):761-6. ).<br>
><br>
> In particular, I refer to some topic details reported here:<br>
><br>
> *...The MD simulation was performed using [...] CHARMM 32a216 [...] 15<br>
> attempts to generate a MD trajectory without applying nuclear Overhauser<br>
> enhancement (NOE) restraints led to a loss of the secondary structure of<br>
> TM7. For this reason the first 5 ns of the MD were performed with the NOE<br>
> restraints applied for the distances between the backbone carbonyl oxygen<br>
> atom of the residue n and the backbone NH-group of the residue n+4 of<br>
> TM7[...]The restraints were applied to all the residues, with the<br>
> exception<br>
> of the prolines and residues immediately following [...]That constraint<br>
> preserved the helical structure of TM7, which remained stable after<br>
> removing<br>
> the NOE restraints. [...] After 5 ns the MD simulation was continued<br>
> without<br>
> any restraints...*<br>
><br>
> How can I do it with Gromacs?<br>
><br>
> I suppose that I also could manually provide classical distance<br>
> restraints,<br>
> defining arbitrary Hbond cutoffs instead of NOE distance restraints, but a<br>
> such alternative sounds less elegant to me.<br>
<br>
</div></div>There's a whole section in the manual on such restraints. Please start by<br>
reading there and come back with specific questions.<br>
<br>
Mark<br>
<br>
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