[gmx-users] Negative arginine?

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 2 09:09:31 CET 2004

On Wed, 2004-12-01 at 16:32 -0600, Eric Jakobsson wrote:
> 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.
I agree. The proper thing to do is a quantum calculation, first to see
where the proton is (many possibilities!) and second to determine the
charge. Then one should wonder how fast such an Arginine in solvent
would gobble up a new proton (or two)...

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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