Structure Refinement Using XPLOR-NIH
Introduction
Here we describe the protocol for Xplor-NIH refinement of NMR structures. The Xplor-NIH molecular structure determination package is available at http://nmr.cit.nih.gov/xplor-nih/[1][2]
The restrained simulated annealing protocol uses many of the updated features of the Xplor-NIH software, including:
- the IVM module for torsion angle and rigid body dynamics
- a radius of gyration term to represent the weak packing potential
- database potentials of mean force to refine against:
- Cα/Cβ chemical shifts
- multidimensional torsion angles,
- backbone hydrogen bonding database
- RDCs can be included but aren't described here
The topology and parameter files protein.top and protein.par, which were designed to agree with bond lengths and angles from the CSDX force field, are used.
Protocol
Setup
The files needed to run the Xplor-NIH refinement are:
- prot_noe.tbl
- prot_dihe.tbl
- prot_hbond.tbl (optional)
- prot_shiftsCACB.tbl
- prot.psf (described below), can be obtained from mkpsf_prot.inp
- sa_refine.inp (edited to reflect your protein parameters)
- xplor format PDB files to be refined (described below)
I. The first four files needed are NMR restraints in Xplor/CNS format.
If you have restraint files in another format, one way to convert is using PDBStat (reference)
II. Creating protein structure file, (psf), using mkpsf_prot.inp script
The X-Plor psf file specifies the atom parameters and connectivity for all amino acids. The xplor script mkpsf_prot.inp is edited with the protein sequence in three letter code and used to generate the psf files by running:
xplor < mkpsf_prot.inp > temp.out
Download the script mkpsf_prot.inp.
References
- ↑ Schweiters, C.D.; Kuszewski, J.J.; Tjandra, N.; Clore, G.M. “The Xplor-NIH NMR Molecular Structure Determination Package,” J. Magn. Reson. 2003, 160,66-74
- ↑ Schweiters, C.D.; Kuszewski, J.J.; Clore, G.M. “Using Xplor-NIH for NMR molecular structure determination,” Progr. NMR Spectroscopy. 2006, 48, 47-62