[gmx-users] Negative arginine?
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,
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
> 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.
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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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