[gmx-users] Negative arginine?
jake at ncsa.uiuc.edu
Wed Dec 1 23:32:54 CET 2004
I don't see what can be learned by arbitrarily making up charge
assignments, since they will almost certainly be incompatible with any
possible electronic structure for the molecule.
At 05:09 PM 11/29/2004 -0800, you wrote:
>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
> > > 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.
> > ________________________________________________________________________
> > 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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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda,
Maryland, to be Director of the NIGMS Center for Bioinformatics and
Computational Biology and Chair of the NIH Biomedical Information Science
and Technology Initiative Consortium, but maintaining my research lab at
Illinois by periodic commuting. My usual schedule is four days a week at
NIH and three days a week at Illinois.)
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