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
Received on Thu Oct 31 2002 - 11:22:17 PST
