+++ /dev/null
- ----------------
- UNRESPACK v. 3.0
- ----------------
-
-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).
-
-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.
-
-The package has the following directory structure
-
-unrespack-v.3.0
- |
- |---------doc (documentation)
- |
- |---------PARAM (force field parameters)
- |
- |---------source
- | |
- | |-----unres (UNRES source codes; various versions)
- | | |
- | | |---src_MIN (only energy evaluation and minimization)
- | | |---src_CSA (all functions except MD, includes CSA)
- | | |---src_MD (all functions except CSA, includes MD, single chains)
- | | |---src_MD-M (all functions except CSA, includes MD, oligomeric proteins)
- | |-----wham (weighted analysis method source codes)
- | | |
- | | |---src (single chains)
- | | |---src-M (oligomeric proteins)
- | |
- | |-----cluster (cluster analysis source coded)
- | | |
- | | |---clust-unres
- | | | |
- | | | |----src (input data from UNRES)
- | | |
- | | |---clust-wham (input data from WHAM)
- | | |
- | | |----src (for single-chain proteins)
- | | |----src-M (for oligomeric proteins)
- | |
- | |-----xdrfpdb (file format conversion source codes)
- | |
- | |---src (single chains)
- | |---src-M (oligomers)
- |
- |----------bin (C-shell script, batch scripts, and pre-compiled binaries)
- | |
- | |-----unres
- | | |
- | | |---CSA
- | | |---MD
- | |
- | |-----wham
- | |-----cluster
- | |-----xdrfpdb
- |
- |--------examples
- |
- |-----unres
- |-----wham
- |-----cluster
-
-The distribution files and directories are the following:
-
-unrespack-v.3.0.tar.gz - gzipped tarfile of the entire package, with directory
- structure as above.
-
-unres-src-v.3.0.tar.gz - UNRES source codes; uncompresses to give the directories
- with UNRES source codes (src_CSA, src_MD, src_MD-M)
-
-wham-src-v.3.0.tar.gz - WHAM source codes; uncompresses to give the directories
- with WHAM source codes (src and src-M)
-
-cluster-src-v.3.0.tar.gz - CLUSTER source codes; uncompresses to give the
- diresctories with CLUSTER source codes (clust-unres/src, clust-wham/src
- and clust-wham/src-M)
-
-xdrfpdb-v.3.0.tar.gz - XDRFPBD source codes; uncompresses to give the xdrfpdb
- directory
-
-unrespack-bin-v.3.0.tar.gz - UNRES binaries; uncompresses to give the bin
- directory and subdirectories with the elements of the package.
-
-unrespack-examples-v.3.0.tar.gz - examples; uncompresses to give the examples
- directory and subdirectories.
-
-PARAM.tar.gz - force field parameters; uncompresses to give PARAM directory
-
-unrespack-doc-v.3.0.tar.gz - all documentation; uncompresses to give the doc
- directory.
-
-To uncompress a tar-gz file of a package say:
-
-gzip -cd package.tar.gz | tar xf -
-
-Each directory contains a READMRE file to explain its contents.
-
-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.
projects / unres.git / blobdiff