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duarte |
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reconstruct |
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Protein contact map reconstruction using the TINKER package |
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duarte |
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http://www.molgen.mpg.de/~lappe/reconstruct |
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duarte |
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INSTALLATION |
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You need Java 1.6 or newer (available from http://java.sun.com). |
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1. Get TINKER and PRM files from http://dasher.wustl.edu/tinker/ |
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Linux TINKER executables are available at: |
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http://dasher.wustl.edu/tinker/downloads/linux.tar.gz |
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Force Field Parameter files are available at: |
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http://dasher.wustl.edu/tinker/distribution/params/ |
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Unfortunately TINKER is written in statically allocated FORTRAN so |
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memory is allocated at program startup and there must be enough of it |
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available or the program will fail. The allocation sizes are controlled |
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by static variables in sizes.i file (in the TINKER source distribution). |
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The default binaries provided in the TINKER web site are |
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compiled with too restrictive static values. In practice this means that |
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the "distgeom" program will only run for very small proteins. |
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Thus in order to be able to run the reconstruct program for reasonably |
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sized proteins you will need to download the TINKER source code at: |
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http://dasher.wustl.edu/tinker/downloads/tinker-5.1.02.tar.gz |
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modify the sizes.i constants file and recompile it. |
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The parameters to modify are MAXGEO and MAXATM and MAXKEY. |
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Values MAXATM=100000, MAXGEO=10000 and MAXKEY=20000 should suffice. These |
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values would already require a memory allocation of >1GB |
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If the programs can not run because they can't allocate enough memory one |
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work-around is to increase the size of your swap file. TINKER only |
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allocates a lot of memory at startup but most of the time doesn't actually |
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use most of it. |
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2. Edit the file reconstruct.cfg and set the parameters TINKER_BIN_DIR and |
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PRM_FILE. The only type of PRM_FILE supported is AMBER force field |
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parameter files. |
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A per-user reconstruct.cfg file can be placed in the user's home |
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directory. |
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3. Run it |
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./reconstruct |
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PARALLEL VERSION, SUN GRID ENGINE |
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For the parallel version to work (option -A) the path to the SGE root directory |
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needs to be set in the reconstruct shell script (sgeroot variable) |
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CONTACT MAP FILES |
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The contact map files that the reconstruct program reads are simple text files with |
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a few headers and 3 columns: 1st for i residue numbers, 2nd for j residue numbers and |
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3rd for weights (currently ignored). |
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An example file is provided: sample.cm (Cbeta 8A cutoff contact map for PDB 1bxy, chain A) |
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The format is the same used by our CMView contact map visualization program (see |
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http://www.molgen.mpg.de/~lappe/cmview) |
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The headers are essential for the reconstruct program to work. The parameters of the |
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contact map: SEQUENCE, CONTACT TYPE (CT) and CUTOFF are read from the headers. |
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