[gmx-users] grompp warnings "Overriding atomtype ..."

[Leandro Bortot]

Dear all,

     I am trying to do a glycoprotein simulation with GROMACS using the
AMBER99SB-ILDN forcefield together with GLYCAM06.

     After constructing my glycoprotein grompp gives the following warning
for most of the atomtypes defined in the .itp file with the glycoprotein
parameters:

          WARNING 23 [file glycoprot.itp, line 27]:
          Overriding atomtype CC


     Is this supposed to be this way?

     Because there are new definitions of atomtypes which are not used in
the carbohydrate nor in the glycosylated residue, I suppose that these
parameters are really meant to override the default ones since they are
only necessary for water and ions. Am I right?


thank you in advance,
Leandro Bortot