SciCombinator

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Concept: GROMACS

166

Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package.

Concepts: Protein structure, Amino acid, Molecular biology, Molecular dynamics, Posttranslational modification, GROMACS, GROMOS

153

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

Concepts: Molecular dynamics, Lipid, Molecular mechanics, CHARMM, Force field, GROMACS, Force field implementation, OPLS

149

In this data article we provide topologies and force field parameters files for molecular dynamics simulations of lipids in the OPLS-aa force field using the GROMACS package. This is the first systematic parameterization of lipid molecules in this force field. Topologies are provided for four phosphatidylcholines: saturated DPPC, mono-cis unsaturated POPC and DOPC, and mono-trans unsaturated PEPC. Parameterization of the phosphatidylcholines was achieved in two steps: first, we supplemented the OPLS force field parameters for DPPC with new parameters for torsion angles and van der Waals parameters for the carbon and hydrogen atoms in the acyl chains, as well as new partial atomic charges and parameters for torsion angles in the phosphatidylcholine and glycerol moieties [1]. Next, we derived parameters for the cis and trans double bonds and the neighboring them single bonds [2]. Additionally, we provide GROMACS input files with parameters describing simulation conditions (md.mdp), which are strongly recommended to be used with these lipids models. The data are associated with the research article “Cis and trans unsaturated phosphatidylcholine bilayers: a molecular dynamics simulation study” [2] and provided as supporting materials.

Concepts: Molecular dynamics, Atom, Chemical bond, Lipid, Lipid bilayer, Lecithin, GROMACS, OPLS

26

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged both by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the last few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA and CGenFF force fields and four different water models, and by including the often neglected polarization costs we show that the common charge models are somewhat underpolarized.

Concepts: Mathematics, Molecular dynamics, AMBER, CHARMM, Force field, GROMACS, Force field implementation, OPLS

25

Bromomethane (CH3Br) is an acutely toxic environmental pollutant that contributes to ozone depletion. Molecular simulation could be a valuable tool for studying its partitioning and transport in the environment if an accurate molecular model was available. The Generalized Amber Force Field (GAFF), OPLS (Optimized Potentials for Liquid Simulations) force field, and CHARMM General Force Field (CGenFF) were tested for their ability to model the physical properties of liquid bromomethane. The OPLS force field was in fairly good agreement with experiment, while CGenFF and GAFF were significantly in error. The Br Lennard-Jones parameters of the GAFF and CGenFF models were reparameterized, but their radial distribution functions still have significant deviations from those calculated by Ab Initio Molecular Dynamics (AIMD). A Drude polarizable force field for bromomethane was parameterized with an off-center positively charged site to represent the C-Br σ-hole. This model is in good agreement with the bulk physical properties and the AIMD RDFs. The modest solubility of bromomethane was reproduced by this model, with dispersion interactions being the dominant water-solute interaction. The water- solute electrostatic interactions are a smaller factor in solubility. This model predicts bromomethane to have a 13 kJ/mol surface excess potential at the water-vapor interface.

Concepts: Electric charge, Molecular dynamics, Computational chemistry, Molecular modelling, Molecular mechanics, AMBER, Force field, GROMACS

24

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM-format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities, and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

Concepts: Molecular dynamics, AMBER, CHARMM, Force field, GROMACS, OPLS, NAMD, Molecular dynamics software

23

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc.

Concepts: Molecular dynamics, Ring, AMBER, CHARMM, GROMACS, Force field implementation, OPLS, Molecular dynamics software

0

Flock House virus (FHV) is a well-characterized model system to study infection mechanisms in non-enveloped viruses. A key stage of the infection cycle is the disruption of the endosomal membrane by a component of the FHV capsid, the membrane active γ peptide. In this study, we perform all-atom molecular dynamics simulations of the 21 N-terminal residues of the γ peptide interacting with membranes of differing compositions. We carry out umbrella sampling calculations to study the folding of the peptide to a helical state in homogenous and heterogeneous membranes consisting of neutral and anionic lipids. From the trajectory data, we evaluate folding energetics and dissect the mechanism of folding in the different membrane environments. We conclude the study by analyzing the extent of configurational sampling by performing time-lagged independent component analysis.

Concepts: Protein, Protein structure, Virus, Molecular dynamics, Analysis, PlayStation 3, GROMACS, Folding@home

0

In molecular dynamics or Monte-Carlo simulations, the interactions between the particles (atoms) in the system are described by a so-called force field. The empirical functional form of classical fixed-charge force fields dates back to 1969 and remains essentially unchanged. In a fixed-charge force field, the polarization is not modeled explicitly, i.e. the effective partial charges do not change depending on conformation and environment. This simplification allows, however, a dramatic reduction in computational cost compared to polarizable force fields and in particular quantum-chemical modeling. The past decades have shown that simulations employing carefully parametrized fixed-charge force fields can provide useful insights into biological and chemical questions. This overview focusses on the four major force-field families, i.e. AMBER, CHARMM, GROMOS and OPLS, which are based on the same classical functional form and are continuously improved to the present day. The overview is aimed at readers entering the field of molecular simulations. More experienced users may find the comparison and historical development of the force-field families interesting.

Concepts: Molecular dynamics, Chemistry, Computational chemistry, Molecular mechanics, AMBER, Force field, GROMACS, Force fields

0

A new method for switching between structures consisting of equivalent discrete and flexible objects with different particle representation and object configuration, including different resolution levels (number of particles per object), is reported. The method is fully general since it does not require any extra code nor additional database elements for new systems. It is based on a Monte Carlo sampling of the configurational space for each object type of the target system, which is controlled by a Metropolis acceptance criterion of movements (translations, rotations and relative deformations of the object configuration) based on the generalized distance between the sets of particles at both representations. For Gaussian distributed distances, such minimization procedure is equivalent to an optimization of Χ2 in a maximum likelihood method. This provides sound statistical support since the method leads to the statistically most probable configuration of the system at each representation. The configurations obtained in this way are then used to create resolution exchange maps for each object type, which allows the extrapolation of the conversion to every object configuration throughout the whole system. As an example, the method is here tested with several molecular dynamics simulated systems (ionic liquids, cyclodextrins, cell-penetrating peptides, cyclic peptides, lipid bilayers, vesicles, heterogeneous organic molecules, DNA and solvated proteins) for different resolution forcefields (GROMOS, AMBER, OPLS, MARTINI) using Gromacs. In this context, the method can be applied to map structures described by any other pair of force fields, as well as to homogeneous and heterogeneous systems with many different molecules. The method is proved to be highly eficient since the time required for the mapping is practically independent of the number of molecules in the target system.

Concepts: Protein, Molecular dynamics, Maximum likelihood, Monte Carlo, Monte Carlo method, Object-oriented programming, Force field, GROMACS