[gmx-users] dihedral restraints with CVS version -- has anyone used dihedral restraints? Do they work?
spoel at xray.bmc.uu.se
Tue Jun 7 19:28:31 CEST 2005
On Tue, 2005-06-07 at 10:14 -0700, David Mobley wrote:
> I previously inquired about imposing dihedral restraints in GROMACS.
> David responded that I can do this with the CVS version of Gromacs. We
> have the CVS version from April 4 and I have been trying to impose
> dihedral restraints between a protein and a small molecule (two atoms
> in the protein and two in the small molecule, for example).
> I know how to implement restraints -- I can do angle and distance
> restraints fine. But when I use dihedral restraints, I consistently
> get a restraint energy of 0 regardless of how strong I make the
Can you send me a tpr file?
> Can any developers verify whether the dihedral restraints are known to
> actually work? Or have any users on this list actually successfully
> used these restraints?
> I would appreciate a response. I've e-mailed the list several times
> about this and been ignored. I don't know whether it's that people
> assume I'm making some stupid mistake and don't want to take the time
> to answer my question, or whether someone knows this is a problem and
> doesn't want to admit it, or...
> I'm about to give up on Gromacs and go back to using AMBER, even
> though it's slower, since at least it works. But I figured I should
> give this one more try.
> David Mobley
> UC San Francisco
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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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