http://cgmartini.nl/index.php/martini-3-tutorials/parameterizing-a-new-small-moleculecgmartini.nl/index.php/martini-3-tutorials/parameterizing-a-new-small-molecule 0. Introduction 本教程将讨论如何为新的小分子构建Martini 3.0拓扑。该教程基于Martini 2教程,但加入了Martini 3.0中的一些更改。建议阅读...
Martini 3 small-molecule database database molecular-dynamics coarse-graining martini3 small-molecules Updated Aug 21, 2024 Shell MikkelDA / COBY Star 20 Code Issues Pull requests Discussions COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3 coa...
Protein-small molecule binding? 2024Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the organization of protein macro-complexes, and even the interaction of proteins with other molecules. The Martini force ...
We have previously shown that Martini 3 simulations of IDPs produce overly compact conformational ensembles, resulting in poor agreement with small-angle X-ray scattering (SAXS) and paramagnetic relaxation enhancement (PRE) experiments7. Using an approach inspired by previous work on assessing and reba...
because the interaction parameters are not specific to a particular molecule or class of molecules, the MARTINI force field may not capture the important interactions between atoms in a given molecule. Additionally, because the non-bonded interaction parameters are optimized to free energy data, the ...
(3) realistic representation of conformational flexibility of each molecule in the system; (4) accurate thermodynamics and kinetics of binding. Currently, none of the CG force fields available fulfills all the requirements listed above. The examples showed in this work indicate that the current ...
--mol MOLNAME Name of CG molecule --aa AA filename of all-atom structure .gro file --cg CG filename of coarse-grained structure .gro file --top TOPFNAME filename of output topology file -v, --verbose increase verbosity --fpred Atomic partitioning prediction ...
3 nm margin between PEI-CA and the edge of the box. The lipid bilayer was generated using CHARMM-GUI72,73,92with the samex-ydimensions. For the systems involving siRNA or SP-B, thexandydimensions of the box were sized to allow for a 1.5 nm margin around the largest molecule. A ...
By default, mode is set to 'run', which computes the MARTINI forcefield for a given molecule.To display the usage-information (help), either supply -h, --help, or nothing to auto_martini:usage: auto_martini [-h] [--mode {run,test}] [--sdf SDF | --smi SMI] [--mol MOLNAME]...
crystals can also impart advantages in packaging and handling operations. Conventional crystal purification methods are generally restricted to molecule that are thermally stable at high temperatures, and this common drying techniques can be ineffective for thermally unstable and crystalline solvated compounds...