Input file

[zyh4482]

Hi. I'm new in molecular dynamics. May I ask several silly questions?

1. How to generate the input file with MDtraj format like .xct and .gro?
2. If the target protein does not have crystal structure (but two family members which have PDB data show similarity), how could I analyze the interaction between lipid and target protein? Thank you so much.

[robincorey]

Hi - thanks for your interest. Here are some answers to your questions:

1. Typically these would be generated using a MD program like gromacs, which has many decent tutorials online.
2. You can either use a similar PDB, or try and build a model of your system, either based on homology to an existing PDB (e.g. using https://swissmodel.expasy.org/) or AlphaFold (https://alphafold.ebi.ac.uk/ or https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb)

Once you have your protein model, simulations can be setup using a number of methods, inlcuding: https://colab.research.google.com/github/pstansfeld/MemProtMD/blob/main/MemProtMD_insane.ipynb and https://charmm-gui.org/