5 A package to run united-residue protein simulations with the UNRES force field.
6 It is a successor of earlier more specific version of UNRES to predict
7 protein structure by global optimization (v. 1.0) and of the molecular dynamics
13 * This software is provided free of charge to academic users, subject to the
14 condition that no part of it be sold or used otherwise for commercial
15 purposes, including, but not limited to its incorporation into commercial
16 software packages, without written consent from the authors. For permission
17 contact Prof. H. A. Scheraga, Cornell University.
19 * This software package is provided on an "as is" basis. We in no way warrant
20 either this software or results it may produce.
22 * Reports or publications using this software package must contain an
23 acknowledgment to the authors and the NIH Resource in the form commonly used
26 The package has the following directory structure
30 |---------doc (documentation)
32 |---------PARAM (force field parameters)
36 | |-----unres (UNRES source codes; various versions)
38 | | |---src_MIN (only energy evaluation and minimization)
39 | | |---src_CSA (all functions except MD, includes CSA)
40 | | |---src_MD (all functions except CSA, includes MD, single chains)
41 | | |---src_MD-M (all functions except CSA, includes MD, oligomeric proteins)
42 | |-----wham (weighted analysis method source codes)
44 | | |---src (single chains)
45 | | |---src-M (oligomeric proteins)
47 | |-----cluster (cluster analysis source coded)
51 | | | |----src (input data from UNRES)
53 | | |---clust-wham (input data from WHAM)
55 | | |----src (for single-chain proteins)
56 | | |----src-M (for oligomeric proteins)
58 | |-----xdrfpdb (file format conversion source codes)
60 | |---src (single chains)
61 | |---src-M (oligomers)
63 |----------bin (C-shell script, batch scripts, and pre-compiled binaries)
80 The distribution files and directories are the following:
82 unrespack-v.3.0.tar.gz - gzipped tarfile of the entire package, with directory
85 unres-src-v.3.0.tar.gz - UNRES source codes; uncompresses to give the directories
86 with UNRES source codes (src_CSA, src_MD, src_MD-M)
88 wham-src-v.3.0.tar.gz - WHAM source codes; uncompresses to give the directories
89 with WHAM source codes (src and src-M)
91 cluster-src-v.3.0.tar.gz - CLUSTER source codes; uncompresses to give the
92 diresctories with CLUSTER source codes (clust-unres/src, clust-wham/src
95 xdrfpdb-v.3.0.tar.gz - XDRFPBD source codes; uncompresses to give the xdrfpdb
98 unrespack-bin-v.3.0.tar.gz - UNRES binaries; uncompresses to give the bin
99 directory and subdirectories with the elements of the package.
101 unrespack-examples-v.3.0.tar.gz - examples; uncompresses to give the examples
102 directory and subdirectories.
104 PARAM.tar.gz - force field parameters; uncompresses to give PARAM directory
106 unrespack-doc-v.3.0.tar.gz - all documentation; uncompresses to give the doc
109 To uncompress a tar-gz file of a package say:
111 gzip -cd package.tar.gz | tar xf -
113 Each directory contains a READMRE file to explain its contents.
115 CREDITS TO DEVELOPERS OF CODES IMPORTED INTO UNRES
116 --------------------------------------------------
118 All programs use the fitsq subroutine written by Dr. Kenneth D. Gibson,
119 Cornell University, retired.
121 The MD program uses the surfatom subroutine written by Dr. J.W. Ponder,
122 Washington University.
124 The SUMSL subroutine (Gay, Assoc. Comput. Math. Trans. Math. Software, 9,
125 503-524, 1983, is used for minimization.
127 The CLUSTER program uses the hc subroutine developed by Dr. G. Murtagh,
128 ESA/ESO/STECF, Garching.
130 UNRES, WHAM, CLUSTER, and XDRFPDB use the Europort Data Library (xdrf) developed
131 by Dr. F. van Hoesel, Groeningen University, to write and read compressed data