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UNRESPACK v. 3.2 - a package to run united-residue protein simulations with the UNRES force field. It is a successor of earlier more specific version of UNRES to predict protein structure by global optimization (v. 1.0) and of the molecular dynamics version (version 2.0).

The package has the following directory structure:

directory tree after unpacking

Before downloading this package you must agree on the License Terms as stated below.

LICENSE TERMS

  • This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact Prof. H. A. Scheraga, Cornell University.
  • This software package is provided on an "as is" basis. We in no way warrant either this software or results it may produce.
  • Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.

To uncompress a tar-gz file of a package say:

gzip -cd package.tar.gz | tar xf -

Each directory contains a README file to explain its contents.


NARES

This is a preliminary distribution of the NARES software for coarse-grained simulations of nucleic acids with the NARES-2P force field. The functions of the package are as follows:

  1. Single energy evaluation
  2. Energy minimization
  3. Molecular dynamics and its REMD and MREMD extensions
  4. Calculation of thermodynamics properties and conformational ensembles
  5. Cluster analysis of conformational ensembles

Please refer to the UNRES manual and to the examples collected in the TESTS director for more detail; except for different sequence encoding the input format is the same.

Source code:

nares: main components of the package (MD, (M)REMD, energy evaluation and minimization).
wham: weighted-histogram analysis of (M)REMD results.
cluster: cluster analysis of the ensembles generated by (M)REMD and analyzed by wham.
xdrf2pdb: produce pdb-format trajectories from compressed trajectory files (cx).

References:

  1. Y. He, M. Maciejczyk, S. Oldziej, H.A. Scheraga, A. Liwo,
    Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix.
    Phys. Rev. Lett., 110, 098101, 2013
  2. A. Liwo, M. Baranowski, C. Czaplewski, E. Golas, Y. He, D. Jagiela, P. Krupa, M. Maciejczyk, M. Makowski, M.A Mozolewska, A. Niadzvedtski, S. Oldziej, H.A. Scheraga, A.K. Sieradzan, R. Ĺšlusarz, T. Wirecki, Y. Yin, B. Zaborowski.
    A unified coarse-grained model of biological macromolecules based on mean-field multipole.multipole interactions.
    J. Molec. Model., 2014, 20, 1-15.

You can download this preliminary distribution of the NARES software here.


CREDITS TO DEVELOPERS OF CODES IMPORTED INTO UNRES

  • All programs use the fitsq subroutine written by Dr. Kenneth D. Gibson, Cornell University, retired.
  • The MD program uses the surfatom subroutine written by Dr. J.W. Ponder, Washington University.
  • The SUMSL subroutine (Gay, Assoc. Comput. Math. Trans. Math. Software, 9, 503-524, 1983, is used for minimization.
  • The CLUSTER program uses the hc subroutine developed by Dr. G. Murtagh, ESA/ESO/STECF, Garching.
  • UNRES, WHAM, CLUSTER, and XDRFPDB use the Europort Data Library (xdrf) developed by Dr. F. van Hoesel, Groeningen University, to write and read compressed data files.

Previous versions ("version 2") of the packages are available here.