[gmx-users] Noe distance restraints

Mark Abraham mark.abraham at anu.edu.au
Fri Feb 29 11:08:56 CET 2008

> 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.


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