g-mmpbsa 3.0.9

MM/PBSA calculations for GROMACS.

Introduction

g_mmpbsa is developed using two widely used open source software i.e. GROMACS and APBS and it has similar user interface like other GROMACS tools. It is now upgraded as Python package for easy installation and usage.

g_mmpbsa contains several sub-commands to carry out binding energy calculation using MM/PBSA method and energetic contribution of each residue to the binding using energy decomposition scheme.

Now g_mmpbsa can be directly installed on Linux and MacOS using pip or pipx and it supports all the GROMACS versions.

For complete documentation, please visit g_mmpbsa.

Please post problems and queries in g_mmpbsa forum.

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Please always cite following two publications:

• Kumari et al (2014) g_mmpbsa - A GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model. 54:1951-1962.

• Baker et al. (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98:10037-10041.

• Eisenhaber et al. (1995) The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies J. Comput. Chem. 16:273-284.

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