[gmx-users] atom names

[Carlos Emidio]

Hello gmxs!

We´re trying to perform MD of polysaccharides. As the molucule we´re
interested in has many ramifications, we joined each ramification to its
respective monomer of the "main chain", making it "linear" (i tried to
use specbonds to link the ramifications but i had some problems with
it).
As the atoms names for each residue were all the same, we sticked some
Js and Ts in the beginning of all atom names.
The problem is that genbox didn´t recognize them as Cs or Os, setting
all vdw radius do 0.105 (though its atomtype was specified in .top
file). Also, ngmx showed all atoms pink. How could I solve it? Is that a
big deal? How can i tell  for sure if mdrun used the right vdw
parameters? -- I already gmxdumped the tpr and it seemed alright --