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root/owl/tags/owl-1.9.2/reconstruct/README-reconstruct.txt
Revision: 1365
Committed: Mon Mar 28 16:51:55 2011 UTC (9 years, 2 months ago) by hstehr
File size: 2830 byte(s)
Log Message:
tagging owl-1.9.2 to match CMView-1.9.2-released-as-1.1rc5
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1 duarte 978 reconstruct
2    
3     Protein contact map reconstruction using the TINKER package
4    
5 duarte 979 http://www.molgen.mpg.de/~lappe/reconstruct
6 duarte 978
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