[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:
> Hi!
> 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
> Grazia

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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