X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=doc%2FUNRESPACK.TXT;fp=doc%2FUNRESPACK.TXT;h=0000000000000000000000000000000000000000;hp=5b8fdaf254562bf3380caf3f519ed2b40ad92d19;hb=7e75cfee188bb6255d455c46c87b9f34cf46aa00;hpb=e62983fb4a02b190d8fbfda27a26ec7ce96799d8

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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.