[Xplor-nih] MTSL - parameter and toplogy files

[Charles at Schwieters.org]

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Hello Linda--

> 
> I have used a spin label as a paramagnetic relaxation enhancer to
> obtain distance constraints. I found the instructions for
> incorporating the CYSP residue and all worked fine. However, in every
> structure calculation I find that the nitroxide side chain is in a
> completely extended conformation. ALL dihedrals are 180. For MTSL
> X1=-60, X2=-60 and X3(CB-1SG-2SG-CL1) =+/-90 for at least a start
> (these are from many crystal structures from the Hubbell group)

Looking at cysp.top, I see only one dihedral angle defined- this needs
to be fixed, in the absence of other information. Note that the DIHE
term is normally not used in Xplor-NIH calculations- the RAMA term is
preferred. However, the RAMA database will have no entries for MTSL, so
DIHE will have to be used- probably with a constraint interaction
statement. Do note that protocol.addUnkownAtoms() does invoke the DIHE
term [ protocol.fixupCovalentGeom() does not ].

> 
> The cysp.top file refers to the sulfurs as SG1 and SG2
> 

I don't think there's a conflict with disulfides, other than both CYSP
and CYS specify that the sulfur atom type to be S.

So- please add the dihedral definitions to cysp.top, and the values to
cysp.par, and contact me if you need further help with this.

best regards--
Charles
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