,
"Flamingoes" by Paul Re

DOWNLOADABLE CODES

  • GNU licensing

    Quaternion-based algorithm for calculating RMSD and its gradient

    The code is written in Fortran 90, and has been tested with NAGWare f95 and Portland group pgf90 on Linux systems only.
  • rmsd.tar.gz

    Mirror site:

  • Dill group webpages

    A discussion can be found in
  • Using Quaternions to calculate RMSD (Journal of Computational Chemistry, 2004, vol 25, p 1849)

    Analytical Loop Closure Algorithm

    The code is written in Fortran 90, and has been tested with NAGWare f95 and Portland group pgf90 on Linux systems only.

  • loop-closure.tar.gz

    The same code has been translated into C, thanks to Jae Shick Yang. Plase contact him at jyang@fas.harvard.edu for questions on the C code.
  • loop-closure-c.tar.gz

    Mirror site:

  • Dill group webpages

    This is an implementation of the analytical loop closure algorithm as described in
  • A Kinematic View of Loop Closure (pdf), (ps) (Journal of Computational Chemistry, Volume 25, Issue 4, Pages 510 - 528 (2004) )

    _Biocomp04 presentation (ppt) which solves a polynomial equation to find loop closure solutions. An arbitrary molecular chain can be considered, that includes 6 rotatable bonds, arranged in three coterminal pairs. Any rigid structures can be treated between the pairs of coterminal torsion angles. The bond angle perturbation schemes described in the paper are not included in this distribution.

    This program can be used to find loop structures involving six backbone torsion angles given the position of the two atoms before the loop and two atoms after the loop. For example, in the case of protein, possible structures for a three residue gap can be found given the coordinates of the N and CA atoms of the first residue and the CA ans C atoms of the third residue. Multiple conformations are generated in general (up to 16 conformations are possible in principle).

    Contact the authors ( Vageli Coutsias vageli@math.unm.edu or Chaok Seok chaok@snu.ac.kr ) for any questions
  • Molecular Graph Topology Analyser

  • wb.tar.gz
  • The TIP4P model of water: numerical implementation based on quaternions

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