[gmx-users] residual negative charge?

Victor Manuel Rosas-Garcia quimico69 at yahoo.com
Fri Apr 18 19:17:59 CEST 2008

Hello everybody,

I'm trying to use gromacs to model an aza-type macrocycle (17 atoms around the ring).  The structure does not include any aminoacids or sugars so, I'm building the itp file by hand.  I started with a base topology from the PRODRG server and then added all the missing hydrogens (I want to use OPLS/AA). The problem is that, after assigning all the atom types as best as I could, I end up with a residual charge = -0.034.  The macrocycle itself should be neutral.  Does this mean I need to develop new parameters? Is there any way to fix this without reparametrizing?

Victor M. Rosas García

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