[gmx-users] rephrase my question about torsional restraints
David van der Spoel
spoel at xray.bmc.uu.se
Sat Aug 27 14:33:13 CEST 2005
On Fri, 2005-08-26 at 17:31 -0700, David Mobley wrote:
> 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
> 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.
It only work with protein. But if you add the ligand as an rtp entry in
the force field of your choice, have the protein and ligand be different
chains in the pdb file and run pdb2gmx -ter -merge you have a chance of
making it work.
> 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
> > > _______________________________________________
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> > --
> > 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
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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
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