[gmx-users] neutralization of a charged protein
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 9 09:09:07 CET 2005
Grazia Daminelli wrote:
> I am working with a BMP protein which has an overall charge of -8 and
> the charged residues are 10 LYSH (+) 12 ASP(-) 10 GLU(-) and 4 ARG(+). I
> have put the protein in a box, added water, run a 100 steps minimization
> and then I have used genion to substitute 8 solvent waters with 8 Na+
> ions at the most favorable positions. The result is: 4 Na+ have been
> placed in the vicinity of the protein (GLU and ASP residues) and 4 have
> been aligned along one of the box edges. I wonder if that makes any
> sense. Is there a mistake somewhere? Should I just remove the 4 aligned
> cations? Should I better add x Na+ and y NaCl to have anions in the
> vicinity of positively charged residues and additional Na+ to neutralize
> the system? Comments and suggestions are welcomed
use genion -random
and equilibrate well.
> PS: I am using Gromacs 3.2.1 with G43a1 ff.
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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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