[gmx-users] rephrase my question about torsional restraints

David Mobley dmobley at gmail.com
Wed May 25 18:19:51 CEST 2005


Thanks for the response, but I'm not sure that this is a satisfactory solution:

A) I need to do this in a free energy calculation, so I already have
to use the special CVS version (from Nov. 04) which includes the
reciprocal space part for the free energy calculations.
B) I don't actually want the two molecules to be connected -- I just
need to restrain relative orientations. From looking at the manual, it
looks like the -merge option joins the two molecules, which isn't what
I want (but perhaps I'm misunderstanding it?).

To be a little more specific about what I'm trying to do, I'm doing
some FEP/TI for ligand binding where I first restrain the ligand
relative to some reference atoms in the protein (two angles, three
torsions, and a distance), and then turn off vdw and electrostatics.
I've done some calculations in AMBER, and am now trying to get the
same thing going in GROMACS.

Let me know if this is currently not possible. I suppose another
option is that I simply restrain three different distances rather than
the six dof I'm currently doing, although this will require more


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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