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I will do molecular docking and md simulation using gromacs and autodock
Bioinformatics Analyst RNA Seq, Molecular Docking and MD Simulations
I am a computational Biologist specializing in RNA-Seq transcriptomics, Molecular Docking and Molecular Docking simulations. I work with Linux Bash pipelines, R(DESeq2/Bioconducter), Python and GROMAC...
About this Gig
Welcome to Professional Molecular Docking & MD Simulation Services
Are you looking for rigorous, publication-grade structural biology and computational modeling for your research project? I specialize in protein-ligand molecular docking and all-atom molecular dynamics (MD) simulations using industry-standard tools.
Services Offered
- Molecular Docking (AutoDock Vina):
- Target protein and ligand preparation (PDB/SDF formatting, missing atoms, charges).
- High-precision docking, binding affinity analysis, and ranking.
- 2D and 3D residue interaction profiling (Hydrogen bonds, hydrophobic contacts).
Molecular Dynamics Simulation (GROMACS):
- System setup, solvation, charge neutralization, and force field generation.
- Energy minimization, NVT/NPT equilibrations, and production runs (up to 100 ns+).
- Trajectory Analysis: RMSD, RMSF, Radius of Gyration SASA, and Hydrogen Bond dynamics.
Publication-Ready Deliverables:
- High-resolution 3D rendered figures (PyMOL / UCSF Chimera).
- Complete source code, topology/MDP files, and raw trajectory data (.xtc, .tpr, .edr).
- Comprehensive analytical summary report.
Technology:
Excel
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Google Sheets
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Python
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RStudio
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Zapier
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PowerShell
My Portfolio
FAQ
What file formats or details do I need to provide?
Please provide the PDB ID or .pdb file for your target protein, along with the SMILES string, SDF, or PDB file for your ligand(s).
Will I receive the raw trajectory files from GROMACS?
Yes! In the Standard and Premium packages, all topology, parameter, and trajectory files (.xtc, .tpr, .edr) are delivered alongside the final report.
What force fields do you use for GROMACS MD simulations?
I primarily use CHARMM36 or AMBER (e.g., ff99SB / ff14SB) force fields for proteins, along with CGenFF or AnteChamber/GAFF for ligand topology generation.
What if my protein structure has missing loops or missing residues?
I perform structure cleaning, fix missing side chains, and model missing loops using tools like MODELLER or Swiss-Model before running energy minimization and docking.
