gmx_MMPBSA使用经验
心得体会
1 分钟 读完 (大约 184 个字) 0次访问

gmx_MMPBSA使用经验

　　记录一下gmx_MMPBSA的可视化经验。

工作环境

安装Miniconda

1
2
3
4
5
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

chmod +x Miniconda3-latest-Linux-x86_64.sh

./Miniconda3-latest-Linux-x86_64.sh

安装依赖

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
# 更新conda
conda update conda

# 创建激活gmxMMPBSA环境
conda create -n gmxMMPBSA python=3.11.8 -y -q
conda activate gmxMMPBSA

#安装mpi4py和AmberTools
conda install -c conda-forge "mpi4py=4.0.1" "ambertools<=23.3" -y -q

#安装绘图库
conda install -c conda-forge "numpy=1.26.4" "matplotlib=3.7.3" "scipy=1.14.1" "pandas=1.5.3" "seaborn=0.11.2" -y -q

#安装PyQt6
python -m pip install "pyqt6==6.7.1"

#安装GROMACS
conda install -c conda-forge "gromacs<=2023.4" pocl -y -q

安装gmx_MMPBSA

1
python -m pip install gmx_MMPBSA

使用

准备

参考链接

Installing gmx_MMPBSA

gmx_MMPBSA计算Gromacs分子动力学模拟中的结合自由能

# Cheminformatics, Molecular dynamics, gmx_MMPBSA
A high-throughput mic ... metastatic potential

评论

关注我

链接

分类

标签云

3D cell culture 3D cell culturing 3D cell microarrays 3D culture 3D culture model 3D printing 3D spheroid 3D tumor culture 3D tumors 3D vascular mapping ACT ADV AUTODESK Abdominal wall defects Acoustofluidics Adipocyte Adipogenesis Adoptive cell therapy AirPods Alginate Anticancer Anticancer agents Anticancer drugs Apple Apriori Association Analysis August AutoCAD Autodock Vina Bio-inspired systems Biochannels Bioengineering Bioinspired Biological physics Biomarkers Biomaterial Biomaterials Biomimetic materials Biomimetics Bioprinting Blood purification Blood-brain barrier Bone regeneration Breast cancer Breast cancer cells Breast neoplasms CM1860 CRISPR/Cas9 system CSS CTC isolation CTCs Cancer Cancer angiogenesis Cancer cell invasion Cancer immunity Cancer immunotherapy Cancer metabolism Cancer metastasis Cancer models Cancer screening Cancer stem cells Cell adhesion Cell arrays Cell assembly Cell clusters Cell culture Cell culture techniques Cell mechanical stimulation Cell morphology Cell trapping Cell-bead pairing Cell-cell interaction Cell-laden gelatin methacrylate Cellular uptake Cell−cell interaction Cervical cancer Cheminformatics Chemotherapy Chimeric antigen receptor-T cells Chip interface Circulating tumor cells Clinical diagnostics Cmder Co-culture Coculture Colon Colorectal cancer Combinatorial drug screening Combinatorial drug testing Compartmentalized devices Confined migration Continuous flow Convolutional neural network Cooking Crawler Cryostat Curved geometry Cytokine detection Cytometry Cytotoxicity Cytotoxicity assay DESeq DNA tensioners Data Mining Deep learning Deformability Delaunay triangulation Detective story Diabetic wound healing Diagnostics Dielectrophoresis Differentiation Digital microfluidics Direct reprogramming Discrimination of heterogenic CTCs Django Double emulsion microfluidics Droplet Droplet microfluidics Droplets generation Droplet‐based microfluidics Drug combination Drug efficacy evaluation Drug evaluation Drug metabolism Drug resistance Drug resistance screening Drug screening Drug testing Dual isolation and profiling Dynamic culture Earphone Efficiency Efficiency of encapsulation Elastomers Embedded 3D bioprinting Encapsulation Endothelial cell Endothelial cells English Environmental hazard assessment Epithelial–mesenchymal transition Euclidean distance Exosome biogenesis Exosomes Experiment Extracellular vesicles FC40 FP-growth Fabrication Fast prototyping Fibroblasts Fibrous strands Fiddler Flask Flow rates Fluorescence‐activated cell sorting Functional drug testing GEO Galgame Game Gene Expression Profiling Gene delivery Gene expression profiling Gene targetic Genetic association Gene‐editing Gigabyte Glypican-1 GoldenDict Google Translate Gradient generator Gromacs Growth factor G‐CSF HBEXO-Chip HTML Hanging drop Head and neck cancer Hectorite nanoclay Hepatic models Hepatocytes Heterotypic tumor HiPSCs High throughput analyses High-throughput High-throughput drug screening High-throughput screening assays High‐throughput methods Histopathology Human neural stem cells Human skin equivalent Hydrogel Hydrogel hypoxia Hydrogels ImageJ Immune checkpoint blockade Immune-cell infiltration Immunoassay Immunological surveillance Immunotherapy In vitro tests In vivo mimicking Induced hepatocytes Innervation Insulin resistance Insulin signaling Interferon‐gamma Intestinal stem cells Intracellular delivery Intratumoral heterogeneity JRPG Jaccard coefficient JavaScript July June KNN Kidney-on-a-chip Lab-on-a-chip Laptop Large scale Lattice resoning Leica Leukapheresis Link Lipid metabolism Liquid biopsy Literature Liver Liver microenvironment Liver spheroid Luminal mechanics Lung cells MOE Machine Learning Machine learning Macro Macromolecule delivery Macroporous microgel scaffolds Magnetic field Magnetic sorting Malignant potential Mammary tumor organoids Manhattan distance Manual Materials science May Mechanical forces Melanoma Mesenchymal stem cells Mesoporous silica particles (MSNs) Metastasis Microassembly Microcapsule Microcontact printing Microdroplets Microenvironment Microfluidic array Microfluidic chips Microfluidic device Microfluidic droplet Microfluidic organ-on-a chip Microfluidic organ-on-a-chip Microfluidic patterning Microfluidic screening Microfluidic tumor models Microfluidic-blow-spinning Microfluidics Microneedles Micropatterning Microtexture Microvascular Microvascular networks Microvasculatures Microwells Mini-guts Mirco-droplets Molecular docking Molecular dynamics Molecular imprinting Monolith Monthly Multi-Size 3D tumors Multi-organoid-on-chip Multicellular spheroids Multicellular systems Multicellular tumor aggregates Multi‐step cascade reactions Myeloid-derived suppressor cells NK cell NanoZoomer Nanomaterials Nanoparticle delivery Nanoparticle drug delivery Nanoparticles Nanowell Natural killer cells Neural progenitor cell Neuroblastoma Neuronal cell Neurons Nintendo Nissl body Node.js On-Chip orthogonal Analysis OpenBabel Organ-on-a-chip Organ-on-a-chip devices Organically modified ceramics Organoids Organ‐on‐a‐chip Osteochondral interface Oxygen control Oxygen gradients Oxygen microenvironments PDA-modified lung scaffolds PDMS PTX‐loaded liposomes Pain relief Pancreatic cancer Pancreatic ductal adenocarcinoma Pancreatic islet Pathology Patient-derived organoid Patient-derived tumor model Patterning Pearl powder Pearson coefficient Penetralium Perfusable Personalized medicine Photocytotoxicity Photodynamic therapy (PDT) Physiological geometry Pluronic F127 Pneumatic valve Poetry Polymer giant unilamellar vesicles Polystyrene PowerShell Precision medicine Preclinical models Premetastatic niche Primary cell transfection Printing Protein patterning Protein secretion Pubmed PyMOL Pybel Pytesseract Python Quasi-static hydrodynamic capture R RDKit RNAi nanomedicine RPG Reactive oxygen species Reagents preparation Resistance Review Rod-shaped microgels STRING Selective isolation Self-assembly Self-healing hydrogel September Signal transduction Silk-collagen biomaterial composite Similarity Single cell Single cells Single molecule Single-cell Single-cell RNA sequencing Single‐cell analysis Single‐cell printing Size exclusion Skin regeneration Soft lithography Softstar Spheroids Spheroids-on-chips Staining StarBase Stem cells Sub-Poisson distribution Supramolecular chemistry Surface chemistry Surface modification Switch T cell function TCGA Tanimoto coefficient The Millennium Destiny The Wind Road Thin gel Tissue engineering Transcriptome Transfection Transient receptor potential channel modulators Tropism Tubulogenesis Tumor environmental Tumor exosomes Tumor growth and invasion Tumor immunotherapy Tumor metastasis Tumor microenvironment Tumor response Tumor sizes Tumor spheroid Tumor-on-a-chip Tumorsphere Tumors‐on‐a‐chip Type 2 diabetes mellitus Ultrasensitive detection Unboxing Underlying mechanism Vascularization Vascularized model Vasculature Visual novel Wettability Windows Terminal Word Writing Wuxia Xenoblade Chronicles Xin dynasty XuanYuan Sword Youdao cnpm fsevents gmx_MMPBSA miR-125b-5p miR-214-3p miRNA signature miRanda npm

最新文章

归档

最新文章

归档

Your browser is out-of-date!

Update your browser to view this website correctly. Update my browser now

×