Hi,
> I am trying to use xleap (amber7 version) to make some topology files
> for mm_pbsa.
> The complexes in question contain a modified galactose (sulfated at the
> 3'position) from the Woods parameters (glycam99d). I also have the
> modified version of glycam_99d which contains the sulfate parameters,
> i.e. sulfate torsions. I know that these parameters work in amber5, as
> I have already aquired the trajectories!
>
> When I try to load the pdb of the protein-ligand (sulfated sugar)
> complex I get the following error:
>
> Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> Tried to superimpose torsions for: *-S-O3-* With Sp3 - Sp0
> Sp0 probably means a new atom type is involved
> which needs to be added via addAtomTypes
...
>
> But I don't have any atom types that aren't specified in the parameter
> file!
> And I certainly don't have any Sp0 (sp??) bonds.
>
> Any thoughts....???
>
> Michael Ford
xleap needs to know the hybridization (and element) for a force field
atom type. You need to give this information via addAtomTypes { {"type"
"element" "hybrid"} {...} } explicitly (perhaps you may want to add this
to the addAtomTypes list in your leaprc file); only the specification of
new atom types in the parameter file is not sufficient.
Best regards
Holger
--
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037 USA
phone: +1-858-784-9788
fax: +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++
Received on Thu Oct 31 2002 - 11:54:23 PST
