XPLOR-NIH

New in this release:

• updated default nucleic and protein topology and parameters to use molprobity-based nonbonded term and RNA-ff1 (see eginput/rna). Note: naming of atom O2' is fixed to IUPAC value in these files.
• new ACTUN motif topology and parameters.
• added support for ordered AtomSelections ( rather than taking atom order from the PSF).
• better handling of large structures:
  • handle PDB files with > 100,000 atoms.
  • handle case-dependent segids.

• 3J couplings
• 1J couplings
• 13C shifts
• 1H shifts
• T1/T2
• dipolar couplings
• radius of gyration
• CSA
• solution X-ray and neutron scattering
• refinement using paramagnetic relaxation enhancement spectroscopy
• conformational database torsion angle potentials
• database base-base positioning potentials for DNA
• interface to the NMR graphics package VMD-XPLOR, downloadable separately.
• embedded Python and TCL interpreters.
• addition of Generalized Born code from Tom Simonson .
• support for computing swarms of structures in parallel using multiple computers.
• paramagnetic relaxation enhancement module (Python interface) based on the modified Solomon-Bloembergen equation and multiple structure representation for paramagnetic groups. This module contributed by Junji Iwahara. Please contact him at iwahara-at-helix.nih.gov(replace -at- with a @) for further information.
• The PASD/Marvin facility for automatic NOE assignment.
• the PARArestraints module for including paramagnetism-based NMR restraints in refinement.
• the bin/seq2psf script to generate psf file from sequence.
• includes the isac code for floating RDC alignment tensor.
  H.J. Sass, G. Musco, S.J. Stahl, P.T. Wingfield and S.Grzesiek, J. Biomol. NMR 21: 275-280 (2001).
• merged hbdb code from A. Grishaev. An empirical pseudo-potential that encodes for the relative arrangement of two protein peptidyl units linked by a backbone-backbone hydrogen bond.
• a new CSA potential in the Python interface.
• Removed arbitrary limits on all PSF parameters. Xplor-NIH startup size has been reduced by about 25MB, and it will handle systems as large as your computer's memory will allow.

XPLOR-NIH also includes an new internal variable module (IVM) which allows one to perform efficient molecular dynamics and minimizations using internal coordinates, such as torsion angles. The IVM permits one to do combined torsion angle/rigid body dynamics, torsion angle/cartesian coordinate dynamics, etc. We have found that a 6th order predictory-corrector integrator utilizing a time-varying, automatically time step size provides large computational advantages over the other X-PLOR dynamics engines.

Authors of the NIH extensions:

When publishing work which utilizes Xplor-NIH, please cite:

C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore, "The Xplor-NIH NMR Molecular Structure Determination Package," J. Magn. Res., 160, 66-74 (2003).

C.D. Schwieters, J.J. Kuszewski, and G.M. Clore, "Using Xplor-NIH for NMR molecular structure determination," Progr. NMR Spectroscopy 48, 47-62 (2006).

Documentation

Support

Availability

• executables for multiple Unix platforms.
• various useful parameter and topology files for proteins, dna and dipolar couplings.
• the various databases.
• some examples using most of the refinement tools, IVM torsion angle dynamics, etc. Additional examples are available here .

To obtain the source code of XPLOR-NIH please contact either

Tools for use at NIH.

National Institutes of Health

Department of Health and Human Services