[gmx-users] Noe distance restraints

[Chiara Parravicini]

 Do you refer to pages 58-61 or 148-149 of the manual, about distance
restraints and NMR refinement?

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.

So, should I define arbitrary Hbond cutoffs instead of NOE distance
restraints?

Sorry for being insistent but I cannot come through the question.

 Thanks in advance

 Chiara

On Fri, Feb 29, 2008 at 11:08 AM, Mark Abraham <mark.abraham at anu.edu.au>
wrote:

> > Dear Gromacs users,
> >
> >  I'd like to perform a simulation following the protocol applied in the
> > Ivanov's paper (*Molecular dynamics simulation of the P2Y14 receptor.
> > Ligand
> > docking and identification of a putative binding site of the distal
> hexose
> > moiety.* *Bioorg. Med Chem Lett.* 2007;17(3):761-6. ).
> >
> >   In particular, I refer to some topic details reported here:
> >
> >  *...The MD simulation was performed using [...] CHARMM 32a216 [...] 15
> > attempts to generate a MD trajectory without applying nuclear Overhauser
> > enhancement (NOE) restraints led to a loss of the secondary structure of
> > TM7. For this reason the first 5 ns of the MD were performed with the
> NOE
> > restraints applied for the distances between the backbone carbonyl
> oxygen
> > atom of the residue n and the backbone NH-group of the residue n+4 of
> > TM7[...]The restraints were applied to all the residues, with the
> > exception
> > of the prolines and residues immediately following [...]That constraint
> > preserved the helical structure of TM7, which remained stable after
> > removing
> > the NOE restraints. [...] After 5 ns the MD simulation was continued
> > without
> > any restraints...*
> >
> >  How can I do it with Gromacs?
> >
> > I suppose that I also could manually provide classical distance
> > restraints,
> > defining arbitrary Hbond cutoffs instead of NOE distance restraints, but
> a
> > such alternative sounds less elegant to me.
>
> There's a whole section in the manual on such restraints. Please start by
> reading there and come back with specific questions.
>
> Mark
>
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