[gmx-users] rephrase my question about torsional restraints

[David Mobley]

For the record, I want to follow up on this earlier e-mail from
several months ago. Particularly, I'd been trying to apply torsional
(dihedral) restraints between some atoms in a protein and some atoms
in another small molecule. The correspondence from the list indicated
that, in order for this to work, I needed to have both the protein and
the small molecule in a single molecule file (topology). At the time
this was no problem.

However, recently, I had a ligand I was including with an .itp file
into the protein topology file. Ordinarily, this works fine, but when
I applied some dihedral restraints, I got an error about a residue id
outside the valid range, and remembered this earlier message --
indeed, to apply dihedral restraints, the atoms restrained need to be
within the same topology file.

The suggested solution was to apply pdb2gmx -merge to merge the two
topologies into one. Perhaps this solution is OK generally, but it
turns out not to work well here: I tried running pdb2gmx on a tpr file
containing system information for the protein together with the
ligand, but pdb2gmx can't recognize the ligand (since it's not a
residue) and gives me an error abou AXH (the ligand name) not being a
residue.

Is there another way to merge two topology files into one? Currently
I'm assuming I'll have to manually (or with a script) put the ligand
information into the protein topology file, but if there's a better
way, I'm open to suggestions.

For the record, then, pdb2gmx -merge doesn't work (as far as I can
tell) as a way to merge a protein topology with a small molecule
topology, and so this restriction about having to have both atoms
within the same topology file for dihedral restraints is really a pain
in the neck.

Thanks,
David


On 5/25/05, David <spoel at xray.bmc.uu.se> wrote:
> On Wed, 2005-05-25 at 07:28 -0700, David Mobley wrote:
> > I wrote a question to the list several days ago about torsional
> > restraints (http://www.gromacs.org/pipermail/gmx-users/2005-May/015346.html),
> > and received no response, so let me rephrase:
> >
> > In Gromacs, is there a way (or what is the best way) to impose some
> > torsional restraints between several non-connected atoms -- i.e.,
> > between atoms AB in one molecule and BC in another molecule, to
> > restrain relative orientations of the two molecules? I also need to
> > know the contribution these restraints make to the energy.
> >
> > It is clear from the manual how to do this for distance restraints or
> > angle restraints, but not for torsions.
> You'll have to start with running pdb2gmx -merge on your two chains.
> Then you can restrain any four atoms
> 
> [ dihedral_restraints ]
> i j k l type params
> 
> It's only in CVS AFAIK.
> Try some params and check by running gmxcheck on your topol what you
> get.
> 
> >
> > Thanks,
> > David Mobley
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>