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?
Thanx
Victor M. Rosas García
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