[gmx-users] grompp warnings "Overriding atomtype ..."
jalemkul at vt.edu
Sun Sep 23 05:02:43 CEST 2012
On 9/22/12 10:04 PM, Leandro Bortot wrote:
> 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
> 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?
An atom type of "CC" is certainly nothing to do with water and ions - it's a
carbon atom type. Above you say the warnings are generated from the
glycoprotein topology. That's your problem. The parameters introduced here are
fighting those built into the AMBER99SB-ILDN force field. Atom types are
case-sensitive, so if you truly need new parameters then you can change the case
and they will not override. If the atom type parameters are duplicates of
existing ones, then you can ignore the warning.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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