AMBER has many files that are required to be modified to implement the phoshorylated residues into a structure. First PDB files may need to be converted into AMBER nomenclature and hydrogen atoms added. This is done using the utility protonate which requires PROTON_INFO.
The construction of the prmtop file is done by the AMBER utility leap. We use a leaprc file the contains the directives for the leap program. The new library is appended to the internal datastructures of the program by the directive, loadOff amber_sep.lib.
Finally a MASTER.RST file is constructed from that concatenation of files generated by makeDIST_RST, makeANG_RST, and makeCHIR_RST. The program makeANG_RST uses the new.map and tors.lib databases.
DYANA only requires one file, dyana.lib. The latest phosphoresidue library is called dyana_phos1.lib.
It can be place in either the standard DYANA installation directory or in the your local directory. The key line in your DYANA run file is to include the following path and library name:
MOLMOL has both a core library file which we call amber94.lib from our labs historical connections with AMBER. The MOLMOL residue library is often located at /usr/local/molmol/setup and what every you choose to name the file, it should go in the setup directory. In addition, the simple charge computations in MOLMOL refer to a file called AtomCharge which is also in the setup directory. The file color_atom.mac can also be updated to set the color of phosphurous atoms to magenta.
The command line function InitAll will clear the current MOLMOL database files. The the file menu pulldown command Library --> Read Library will then load the new file. Sometimes you may need to clear old molmol user data in your home directory. This data (~/molmol) can usually be removed. MOLMOL will create a new directory the next time it runs.
The MATLAB scripts were designed to process the initial coordinate outputs from Insight II and orient them by quaternion rotation in the appropriate reference frames for AMBER or DYANA. The MATLAB toolboxes should be installed in user_toolboxes and the path variable in the MATLAB environment can be updated from the File->Set Path menu pull down. The resulting PDB coordinates are required to be inserted in the AMBER and DYANA library files once the proper orientation is obtained from the MATLAB script.
Please refer to each programs file format documentation for proper insertion of the library data or use the standard library files as an example to guide your implementation. We found some out of date information in the DYANA 1.5 manual as applied to our system. Our implementation of amber_sep.lib and dyana_phos1.lib can be used as an example.
The remaining scripts can be included in any convenient location. These include the pdb_renumber awk script that initially is delivered in the ResidueLibTools directory.
The residue backbone atoms (HN-N-CA-C'-O) conformed to the AMBER and DYANA convention that require them to lie in a plane. These rotations were manually implemented in Insight II prior to exporting in the PDB formated file. See the SEP/README.
Questions can be addresses to:
John W Craft Jr
or
Glen Legge
Tel: (713) 743 8380
Fax: (713) 743 2636
University of Houston
Department of Biology and Biochemistry
353 SR2
Houston, Texas 77204-5001
USA
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