Merge branch 'prerelease-3.2.1' into czarek

[unres.git] / doc / 3.1 / ascii-text / UNRESPACK.TXT

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+                                 ----------------
+                                 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.