[gmx-users] Negative arginine?
spronk at its.caltech.edu
Tue Nov 30 02:09:58 CET 2004
What I'm wondering, though: is it at all reasonable to keep all the atoms
there--just change the charges in the molecular topology file so that the
charge group on the side chain now has a total charge of -1 instead of +1?
All the bonding terms and the LJ terms would remain the same; only the
electrostatic interations would change.
Has this sort of thing been done before, for arginine or any other charge
On Tue, 30 Nov 2004, David wrote:
> On Mon, 2004-11-29 at 14:00 -0800, Steven Spronk wrote:
> > Hello all,
> > Has anyone ever attempted to perform an MD simulation by mutating an
> > arginine to a "negative arginine," in other words, making the side chain
> > of a particular arginine -1 instead of +1? In principle, all one would
> > have to do would be to change the charges in the molecular topology file,
> > right?
> And have to know which protons go (one of each NH?, or the HE?), and how
> the geometry changes...
> > If this has been done before, is there some set of charges to place on the
> > atoms so that the arginine's hydrogen bonding behavior is the least
> > perturbed?
> > I know, to be realistic we could simply mutate it to a Glu or Asp, but we
> > thought that a neutral Arg run and a negative Arg run would be interesting
> > controls for our "wild-type" run. Just wondering if there were any
> > references or if anyone has had similar experiences.
> > Thanks,
> > Steve
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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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