[gmx-users] rephrase my question about torsional restraints
spoel at xray.bmc.uu.se
Wed May 25 17:42:15 CEST 2005
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
> David Mobley
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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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