The Ultimate Chemistry
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Software

Script and software development is the essence of computational chemistry.

Below you can find some of my scripts. I will be pleased if you make use of them.

1)  MM2QM

The MM2QM tool has been developed to facilitate a combined docking + MD + QM binding affinity prediction.

The archive contains the source code, the tool compiled under MAC_OS_X_10.7.2_64bits and Ubuntu_11.10_64bits, as well as some example input files.

The tool contains a help module. Below you can also find a short but exhaustive description.

MM2QM was written in C++ with a graphical user interface (GUI) based on the Qt application framework ver. 4.7.4. In the current version (available for Linux and Mac OS) the tool offers access to three main functions: “Simple cut”, “W-M contacts” and “Extract energies” (Fig. 2) The “Simple cut” mode allows one to cut a given protein-ligand complex into ligand-neighboring amino acid pairs, inspect distances between the closest atoms and prepare input files for QM calculations in the Gaussian program. There are three types of jobs covered: SP energy calculation, geometry optimization, and geometry optimization with all heavy atoms frozen. Input files can be created for jobs with or without counterpoise correction.
The procedure starts with reading in a pdb file containing a protein-inhibitor complex. Residues different than water and standard amino acids will be automatically detected. A user has to choose a molecule of interest from a list, and provide a desired cut-off range. All amino acids, for which at least one atom is in the given range, from any of the chosen molecule atoms will be then displayed in a table. After calculation parameters are picked up, input files for QM calculations (containing ligand-neighboring amino acid pairs) can be created. During system decomposition broken peptide bonds are replaced with hydrogens. The script assumes that amino acids are in their standard protonation states. In the “Extract energies” mode one can evaluate on the fly results of QM SP calculations. The only step that has to be followed is to read in a directory containing Gaussian output files. The calculated interaction energies are then displayed in a table. The script recognizes whether calculations were performed with or without counterpoise correction.
The third mode, “W-M contacts”, in principle very similar to the “Simple cut”, was implemented in order to evaluate water-mediated contacts. After reading in coordinates in the pdb format, the complex is cut into smaller parts containing the ligand, neighboring water molecule and an amino acid neighboring with the water molecule. Relevant data are displayed in a table and input files for QM calculations (SP energy calculation, geometry optimization or geometry optimization with all heavy atoms frozen) can be created.


2)  find_min.pl

Helps to restart a Gaussian job when calculation fails to converge and oscillates between several states. The script searches through an output file to find the lowest energy structure. Next it is used to create an input file, root section is copied from and original input file. After you kill the job, execute the scrip:

Input:

./find_min.pl output.log input.gjf

output.log �� interrupted job output file
input.gjf �� interrupted job input file