[gmx-users] neutralization of a charged protein

Grazia Daminelli Grazia.Daminelli-Widany at TU-Berlin.DE
Thu Dec 8 10:33:44 CET 2005


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


PS: I am using Gromacs 3.2.1 with G43a1 ff.

More information about the gromacs.org_gmx-users mailing list