CHARMM‐GUI 10 years for biomolecular modeling and simulation

Abstract

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the molecular details of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project.

MOLECULAR DYNAMICS STUDY OF NON-HYDROGEN-BONDING BASE-PAIR DNA DUPLEX d(GTCDNAM GCGCCGTGGC). d(GCCACGGCGCD5SICSGAC)

“…Orthogonal-box was set to be the unit in periodic boundary condition for further calculation. F19SB-force-field, a nonbonded-cut-off of 10 Å in direct space, were employed to treat longrange-electrostatics interaction by Particle-Mesh-Ewald method (PME)[ [22,23]. In order to keep the parameters consistent with amber-force-field, the force-field parameters for MD simulation of DNAM-D5SICS base-pair was calculated by using ab-initio HartreeFock/QM methodology with 6-31G* basis set [24,25] In which atom-centred-point-charges of the deoxyribose-nucleotides were calculated by using recommended multiple-molecular-fitting and restrained-electrostatic-potential-fitting (RESP) [26] Simulation process involved the following steps: a)-Minimisation b)-Restrained-dynamics to Heat the system from 0-K to 350-K and then 350-K to 300-K, c)-Restrained-dynamics of 10 ns time interval in constant-volume in which restrained-force was gradually decreased by 100 kcal/mole to 0 kcal/mole in 6 steps of 20 kcal/mole/step, d)-Constant-pressure-dynamics of 10 ns to equilibrate the system at 300 K, 10 ns dynamics to fully equilibrate the system and e)-200 ns production-dynamics.…”

Computer simulations of protein–membrane systems

“…To build initial protein-membrane systems for MD simulations in atomistic and CG resolution, the web-based and user-friendly CHARMM-GUI server, 126 developed by Im's group (http://www.charmm-gui.org/), has become widely popular over the last 10 years since the project started in 2006. 187,188 Currently, there are 434 different lipids available for the selection as a membrane component: GPLs, sterols, CLs, PUFAs, SM, detergents, ether-linked GPLs, fatty acids, LPS and glycolipids. There is the possibility to prepare both single-and multicomponent membranes, including the option of varying lipid concentration between the two leaflets.…”

“…There is the possibility to prepare both single-and multicomponent membranes, including the option of varying lipid concentration between the two leaflets. Moreover, the files that are generated by CHARMM-GUI are compatible with several MD engine programs, 164,188,189 including GROMACS, 190,191 AMBER, 192 NAMD, 193 GENESIS, 194 OpenMM, 195 CHARMM/OpenMM, 196 LAMMPS, 197 and Desmond. 198 Several builder and maker programs to create protein-membrane, protein-ligand, and protein-protein systems were developed within CHARMM-GUI.…”

Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III

“…The community of researchers using CHARMM has grown significantly over the past couple of decades, spurred on in more recent years by the advent of a graphical user interface, CHARMM‐GUI (http://www.charmm-gui.org). The paper by Im and collaborators in this issue providing a ten‐year perspective on CHARMM‐GUI is, thus, especially timely.…”