AMBER Archive (2002)

Subject: xleap and modified sugar residues

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Thu Oct 31 2002 - 13:22:17 CST

Hello,

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
Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
Tried to superimpose torsions for: *-C3-O3-*
With Sp3 - Sp0 Sp0 probably means a new atom type is involved
which needs to be added via addAtomTypes
Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
Tried to superimpose torsions for: *-C3-O3-*
With Sp3 - Sp0 Sp0 probably means a new atom type is involved
which needs to be added via addAtomTypes
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
Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
Tried to superimpose torsions for: *-C3-O3-*
With Sp3 - Sp0 Sp0 probably means a new atom type is involved
which needs to be added via addAtomTypes
Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
Tried to superimpose torsions for: *-C3-O3-*
With Sp3 - Sp0 Sp0 probably means a new atom type is involved
which needs to be added via addAtomTypes
Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
Tried to superimpose torsions for: *-C3-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