[gmx-users] Negative arginine?

David spoel at xray.bmc.uu.se
Tue Nov 30 00:38:48 CET 2004

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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