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Simulated Annealing Refinement
The example input files below shows how to refine NMR-derived structures produced by any method inside or outside X-PLOR. The “refine.inp" protocol is of the slow-cooling type reminiscent of the protocol used in crystallographic refinement (see Section 14.1.3). The additional feature included in this protocol is a softening of the van der Waals repulsions. This enables atoms to move through each other. The “refine_gentle.inp" protocol accomplishes the refinement of the coordinates by less dramatic modifications of the energy function. It is intended for under-determined systems where the full empirical energy function is required to determine the final structure of the macromolecule. This applies in particular to structures of short oligonucleotide fragments. Note that the “refine_gentle.inp" protocol uses the standard Lennard-Jones function, electrostatic interactions, and dihedral terms in addition to the conformational energy terms used in the “refine.inp" protocol.
The “refine.inp" protocol is shown below. Important parameters that the user might want to change are the simulated annealing starting temperature and the duration of the cooling stage. The filenames of the family of embedded coordinates are “refine_1.pdb" through “refine_10.pdb". The coordinate files contain useful information about the energies, restraint-satisfaction, and violations. Further refinement can be accomplished by repeated application of this protocol (note that the names of the input and output coordinate sets have to be changed) or by an increase of the cooling period. Repeated application is generally more efficient, because it allows the user to inspect periodically the restraint-statisfaction in the family of refined coordinates and to remove ill-behaved coordinates. This removal of ill-behaved coordinates can be automated by using the acceptance protocol described in the next section.
The “refine_gentle.inp" protocol is show below. In this case two initial DNA structures (“dna_init_1.pdb" and “dna_init_2.pdb") containing ideal A and B-type conformations are refined. Apart from the experimental NOEs, distance restraints for the base-pair hydrogen bonds are included. Note that one can also include planarity restraints (Section 7.3) to maintain the planarity of the base pairs. Average coordinates for the last 10 psec of the molecular dynamics calculation are computed and then refined by conjugate gradient minimization.
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