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XPLOR 3.8 a beta-test version of XPLOR with torsion angle refinement. There is no manual-like for the torsion angle refinement, but you can execute the program and type: dynamics torsion helpor dynamics torsion topology help Remember to set the MAXTREE parameter. This parameter counts the number of disjoint covalent units present in the simulation. Thus a continuous polypeptide chain count as one tree, but so does a water molecule. So if you have 12 molecules per Asymmetric unit then MAXTREE=12. There are two example input files: conventional refinement with torsion angle refinement: /joule2/programs/xplor38/torsion.inpand SA slowcool refinement with torsion angle refinement: /joule2/programs/xplor38/torsion_slow.inp Remember to remove all heavy atoms, water molecules, single atoms or anything that is not linked to the protein. After reading your PDB and PSF you can delete portions of the model with a statement like this:
delete selection=(resid 400 ) end
It runs on all the DEC-ALPHAs; the executable is in: /joule2/programs/xplor38/xplor.exe | ||||||||