Data for: "Martinoid: The Martini Peptoid Force Field"

The contents of the folders are outlined below, for specific information pertaining to a given files relevance please refer to the README.txt file within each sub-directory. The folders are grouped in terms of thier usage within parameterisation process: Bonded Term Mapping: ~~~~~~~~~~~~~~~~~~~~ > Additional Residues - MP2/6-31G(d) torsion scans and atomistic term fitting files for residues NmO, Ns and Nt as well as files for partial charge fitting following the method outlined in the article available at (https://doi.org/10.1021/acs.jpcb.3c03725). > BackboneMapping - all atom (AA) and coarse grained (CG) trajectories and tools for comparison of BB-BB-BB angle term choice at the CG level. > MappingTrajectories - all atom (AA) and coarse grained (CG) trajectories and tools for comparison of BB-BB-BB angle term choice at the CG level for a variety of peptoid trimers. > HelicalOptimisation - all atom (AA) and coarse grained (CG) trajectories and tools for comparison of BB-BB-BB angle and BB-BB-BB-BB dihedral term choice at the CG level for (Nk-Nfes-Nfes)2 helical fragment. > SWARMCGOptimisedITPS - optimised *itp structure files for peptoid dimers as identified by SWARMCG and with which the superimposed parameter sets are generated. > FinalAssemblyAc-Nf-Nf - assessment of impact of parameter superposition for dimer Ac-Nf-Nf, trajectories and measurement tools. Nonbonded Term Mapping: ~~~~~~~~~~~~~~~~~~~~~~~ > AssemblyStudy - single monomer self-assembly study for peptoids to assess the accuracy of bead type selection for these species by assessing whether aggregation occurs/does not occur. > CG_LogD - relevant files for estimating the LogD of various peptoid monomers to assess whether bead choices were sufficently accurate. > HPLC_LogD_Data - chromatograms for peptoid monomers onbtained experimentally using a gradient of H2O : acetonitrile (+ 0.1 % TFA). > NMRCharacterisation - structural validation of pure peptoid monomer material. Model Validation Data: ~~~~~~~~~~~~~~~~~~~~~~ > TrimerAssembly - assembly of Nf-Nke-Nf in form of tape across PBC, this is relevant for comparison to experimnetal Cryo-TEM measurements. > FreeAssemblyNf-Nke-Nf - experimnet to illsutrate 2D bilayer like structures are formed by this trimer, forming the basis for the TrimerAssembly preposition that the nanostriations seen experimnetally are 'tape-like' > NanosheetStudy - validation of parameterisation method using peptoid nanosheet forming oligomers at oil-water interface, validating within a reasonable margin the length of said oligomers in the assembled state. Hamish W. A. Swanson (04.12.23)

各文件夹内容概述如下，若需了解特定文件的相关用途信息，请查阅各子目录内的README.txt文件。本数据集的文件夹按照其在分子力场参数化过程中的功能进行分组：

键合项参数化模块：
> 补充残基（Additional Residues）：包含残基NmO、Ns和Nt的MP2/6-31G(d)扭转扫描与原子级项拟合文件，以及遵循该文献所述方法完成的部分电荷拟合相关文件，文献链接为(https://doi.org/10.1021/acs.jpcb.3c03725)。
> 主链映射（BackboneMapping）：包含全原子（all atom, AA）与粗粒化（coarse grained, CG）轨迹文件，以及用于对比粗粒化层面主链-主链-主链（BB-BB-BB）角度项选择的工具。
> 映射轨迹（MappingTrajectories）：包含多种类肽（peptoid）三聚体的全原子与粗粒化轨迹文件，以及用于对比粗粒化层面BB-BB-BB角度项选择的工具。
> 螺旋优化（HelicalOptimisation）：包含(Nk-Nfes-Nfes)₂螺旋片段的全原子与粗粒化轨迹文件，以及用于对比粗粒化层面BB-BB-BB角度项与BB-BB-BB-BB二面角项选择的工具。
> SWARMCGOptimisedITPS：通过SWARMCG识别得到的类肽二聚体的优化itp格式结构文件，该文件用于生成叠加后的参数集。
> 二聚体Ac-Nf-Nf最终组装评估（FinalAssemblyAc-Nf-Nf）：针对二聚体Ac-Nf-Nf的参数叠加影响评估模块，包含该二聚体的轨迹文件与量化测量工具。

非键合项参数化模块：
> 组装研究（AssemblyStudy）：针对类肽单体的单分子自组装研究，通过观测聚集行为是否发生，验证此类物种的粗粒化珠子类型选择的准确性。
> CG_LogD：包含用于估算多种类肽单体分配系数LogD的相关文件，用于验证珠子选择的准确性是否达标。
> HPLC_LogD数据（HPLC_LogD_Data）：包含通过H₂O:乙腈（含0.1%三氟乙酸(TFA)）梯度洗脱实验获取的类肽单体色谱图。
> NMR表征（NMRCharacterisation）：用于纯类肽单体材料的结构验证。

模型验证数据集：
> 三聚体组装（TrimerAssembly）：Nf-Nke-Nf三聚体以带状形式跨越周期性边界条件（PBC）的组装过程，该数据可用于与实验冷冻透射电子显微镜（Cryo-TEM）测量结果进行对比。
> 自由组装实验（FreeAssemblyNf-Nke-Nf）：用于展示该三聚体可形成二维类双层结构，该结果支撑了TrimerAssembly模块中的前置结论：实验中观测到的纳米条纹为"带状"结构。
> 纳米片研究（NanosheetStudy）：针对在油-水界面形成类肽纳米片的寡聚体开展参数化方法验证，在合理误差范围内验证了组装态下此类寡聚体的长度。

哈米什·W·A·斯旺森（2023年12月4日）