TOPBUILDER

A quantum mechanic-based force field topology generator (TOPBUILDER software) was developed in our group. TOPBUILDER controls docking, quantum mechanics and molecular dynamics simulation software to predict activity of chemical substances in silico. It can also separately output information on flexibility, molecular structure, atoms partial charges and other quantum mechanics calculations data.

Fig.2 Schematic representation of TOPBUILDER-based screening system

We use TOPBUILDER together with GROMACS molecular dynamic package and GAMESS quantum mechanic package to prepare ligands for virtual screening. TOPBUILDER preprocessing system can use sdf, mol2 and pdb formats as input and it output optimized molecular structures in pdbq, mol2, pdb formats. TOPBUILDER also capable to produce molecular topology data for GROMACS and GROMOS96 force fields.

Now TOPBUILDER serves as preprocessor for GROMACS and DOCK software and works as a part of our combined virtual screening system ( Fig. 2 ).

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