Re: xleap and modified sugar residues

From: Holger Gohlke <>
Date: Thu 31 Oct 2002 11:54:23 -0800


> 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


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
Received on Thu Oct 31 2002 - 11:54:23 PST
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