[gmx-users] genbox problems

[K.A. Feenstra]

David wrote:
> 
> On Sun, 2002-08-18 at 14:33, Chris Shaw wrote:
> >
> > Hi all,
> >
> > Just a quick question. I am getting a feel of gromacs by playing around with helices in different solvents. My problem is that genbox re-writes the .gro file to represent the addition of solvent molecules, but doesn't re-write the .top file to reflect the changes. When I attempt to add the .itp file for example dmso.itp into the top file with the #include command it doesn't seem to register and i get an error back re not being able to define SD atom types. Could any one help, as I am sure that i am doing something fundamentally wrong.
> >
> Probably SD is not in the force field you are using for the protein. In
> GROMOS96 the atom types may be named differently. Just check all the
> topology files, including those from the library (gromacs/share/top).
> With the manual in hand it should be straightforward to sort out.

In the Gromos97 ff's (ffG43*) the DMSO atom types are called SDMSO,
CDMSO and ODMSO (as per ffG43a2.atp). We should have edited the dmso.itp
file to be forcefield sensitive, as spc.itp is.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
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