[gmx-users] Noe distance restraints

Chiara Parravicini parravicini.chiara at gmail.com
Fri Feb 29 10:19:25 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.

 Any suggestion will be greatly appreciated!

 Thanks in advance,

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