Supporting CIF Format of Biomolecular Structures in GROMACS

Abstract

In the Protein Data Bank (PDB), the PDB format stands as the major file format for protein structures. However, there are certain intrinsic limitations in the PDB format, such as the storage of structural information in a fixed-width format that would be an issue for very large protein complexes. Therefore, the CIF (crystallographic information framework) format has been proposed, which is characterized by superior expansibility. GROMACS, a widely used software suite for molecular dynamics simulations, currently supports only the PDB format. In this study, we modified the source code of GROMACS, which enables it to support the CIF format structure files as input and subsequently generate molecular topology files. This work simplifies the preprocessing of large protein complexes for MD simulations. Program summaryProgram title: GROMACS-CIF GitHub link to program files: https://github.com/zyzhangGroup/Gromacs-CIF Licensing provisions: GPL-3.0 license Programming language: C++ Nature of problem: GROMACS currently supports only the PDB format but does not support the CIF format of protein structures. For a very large protein complex, the PDB format is not suitable, and only a CIF file is available in the protein data bank. However, the latter cannot be used as a direct input of GROMACS. Solution method: Source codes of the program "pdb2gmx" in GROMACS have been modified by adding several CIF analysis functions parallel to the PDB analysis functions.