[gmx-users] rephrase my question about torsional restraints
spoel at xray.bmc.uu.se
Wed May 25 18:44:54 CEST 2005
On Wed, 2005-05-25 at 09:19 -0700, David Mobley wrote:
> 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?).
You are, it doesn't connect the chains, just merges the two molecules
into one molecule description which is necessary for technical reasons.
> 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.
I'm not sure whether you can perturb dihedral restraints, the other
things should work.
> 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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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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