Hello
I have been trying to get the script for docking 2 protein using chemical
shifts and RDCs to work.
One of my proteins contain Zn2+ ions and I've been able to generate psf-files
for this structure with some help from this mailing list and by modifying
topology and parameter files.
After running the dock_tor_rigid.py and comparing experimental RDCs to RDCs
calculated from the complex, there is very little correlation. Is the alignment
tensor allowed to vary in this protocol or is fixed from the start and
throughout the protocol?
Both of the protein structures in the complex are NMR-structures, solved
without RDC-refinement, where the correlation between my experimental RDCs and
those calculated from the structures are weak. Based on chemical shifts we know
that there is no major structural rearrangement upon complex formation, so
experimental RDCs should agree with the uncomplexed structures.
I tried refining my structures vs the experimental RDCs by using the refine.py
script from the gb1_rdc example and removing NOE, dihedral and hydrogen-bond
restraints.
I don't know if this is the best procedure however, for getting better
agreement with RDCs, since you remove restraints which keep the secondary
structure together.
Based on this refinement, I could get a better agreement with RDCs for the
structure lacking Zn2+. However the same procedure doesn't work for the
structure containing Zn2+, which blows up during refinement.
For the non-Zn2+ structure I use the following command to generate the input
structure (from gb1_rdc/refine.py):
protocol.initParams("protein")
protocol.loadPDB("../1a5ra_cns.pdb")
xplor.simulation.deleteAtoms("not known")
protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
For the Zn2+-structure I use the following commands, which works in the
dock_tor_rigid.py script:
command("param @TOPPAR:parallhdg_new.pro @../param19.ion end")
command("structure @../1tota_cns_zn_t2a.psf end")
command("coor @../1tota_cns_zn_t2a.pdb")
command("coor copy end")
xplor.simulation.deleteAtoms("not known")
protocol.fixupCovalentGeom(maxIters=1000,useVDW=1)
Is there a difference in how RDCs are used in the gb1_rdc/refine.py vs the
dock_tor_rigid.py script?
Also, what is the difference in how the parameters are setup?
The syntax is different, and I can't readily discern what is different.
In the dock_tor_rigid.py script I initialize both structures using the
following commands:
command("param @TOPPAR:parallhdg_new.pro @param19.ion @TOPPAR:par_axis_3.pro
end")
command("structure @1a5ra_cns.psf @1tota_cns_zn_t2a.psf @TOPPAR:axis_500.psf
end")
command("coor @1tota_cns_zn_t2a.pdb")
command("coor @1a5ra_cns.pdb")
command("coor @TOPPAR:axis_xyzo_3.pdb")
command("coor copy end")
Best Regards
Carl Diehl
NNF CPR
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