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root/owl/trunk/reconstruct/README-reconstruct.txt
Revision: 979
Committed: Tue Feb 23 19:03:30 2010 UTC (9 years, 8 months ago) by duarte
File size: 2830 byte(s)
Log Message:
Fixed some issues
Line File contents
1 reconstruct
2
3 Protein contact map reconstruction using the TINKER package
4
5 http://www.molgen.mpg.de/~lappe/reconstruct
6
7 INSTALLATION
8
9 You need Java 1.6 or newer (available from http://java.sun.com).
10
11 1. Get TINKER and PRM files from http://dasher.wustl.edu/tinker/
12
13 Linux TINKER executables are available at:
14 http://dasher.wustl.edu/tinker/downloads/linux.tar.gz
15 Force Field Parameter files are available at:
16 http://dasher.wustl.edu/tinker/distribution/params/
17
18 Unfortunately TINKER is written in statically allocated FORTRAN so
19 memory is allocated at program startup and there must be enough of it
20 available or the program will fail. The allocation sizes are controlled
21 by static variables in sizes.i file (in the TINKER source distribution).
22
23 The default binaries provided in the TINKER web site are
24 compiled with too restrictive static values. In practice this means that
25 the "distgeom" program will only run for very small proteins.
26
27 Thus in order to be able to run the reconstruct program for reasonably
28 sized proteins you will need to download the TINKER source code at:
29 http://dasher.wustl.edu/tinker/downloads/tinker-5.1.02.tar.gz
30 modify the sizes.i constants file and recompile it.
31 The parameters to modify are MAXGEO and MAXATM and MAXKEY.
32 Values MAXATM=100000, MAXGEO=10000 and MAXKEY=20000 should suffice. These
33 values would already require a memory allocation of >1GB
34
35 If the programs can not run because they can't allocate enough memory one
36 work-around is to increase the size of your swap file. TINKER only
37 allocates a lot of memory at startup but most of the time doesn't actually
38 use most of it.
39
40 2. Edit the file reconstruct.cfg and set the parameters TINKER_BIN_DIR and
41 PRM_FILE. The only type of PRM_FILE supported is AMBER force field
42 parameter files.
43 A per-user reconstruct.cfg file can be placed in the user's home
44 directory.
45
46 3. Run it
47 ./reconstruct
48
49
50 PARALLEL VERSION, SUN GRID ENGINE
51
52 For the parallel version to work (option -A) the path to the SGE root directory
53 needs to be set in the reconstruct shell script (sgeroot variable)
54
55 CONTACT MAP FILES
56
57 The contact map files that the reconstruct program reads are simple text files with
58 a few headers and 3 columns: 1st for i residue numbers, 2nd for j residue numbers and
59 3rd for weights (currently ignored).
60 An example file is provided: sample.cm (Cbeta 8A cutoff contact map for PDB 1bxy, chain A)
61 The format is the same used by our CMView contact map visualization program (see
62 http://www.molgen.mpg.de/~lappe/cmview)
63 The headers are essential for the reconstruct program to work. The parameters of the
64 contact map: SEQUENCE, CONTACT TYPE (CT) and CUTOFF are read from the headers.
65