Internal coordinates for molecular dynamics and minimization in structure determination and refinement

J Magn Reson. 2001 Oct;152(2):288-302. doi: 10.1006/jmre.2001.2413.


We present a software module which allows one to efficiently perform molecular dynamics and local minimization calculations in internal coordinates when incorporated into a molecular dynamics package. We have implemented a reference interface to the NIH version of the X-PLOR structure refinement package and we show that the module provides superior torsion-angle dynamics functionality relative to the native X-PLOR implementation. The module has been designed in a portable fashion so that interfacing it with other packages should be relatively easy. Other features of the module include the ability to define rather general internal coordinates, an accurate integration algorithm which can automatically adjust the integration step size, and a modular design, which facilitates extending and enhancing the module.

MeSH terms

  • Algorithms
  • Bacterial Proteins*
  • Magnetic Resonance Spectroscopy*
  • Nerve Tissue Proteins / chemistry*
  • Phosphoenolpyruvate Sugar Phosphotransferase System / chemistry*
  • Protein Conformation
  • Software*


  • Bacterial Proteins
  • G-substrate
  • Nerve Tissue Proteins
  • Phosphoenolpyruvate Sugar Phosphotransferase System
  • phosphocarrier protein HPr
  • phosphoenolpyruvate-glucose phosphotransferase