ENV BASE MODEL DATASET
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This dataset contains structural models and MD simulation data for the
Env base model (BG505 clade A - full-length) inclding glycans N185e and N185h

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model_PDBs
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This folder contains topology (PSF) and coordinate (PDB) files for
initial and equilibrated structures in different system representations.
These are intended for visualization and structural reference.

A) lipids_protein_glycans
   Includes:
   - Protein
   - Glycans (including N185e/h)
   - Membrane lipids
   - No water
   - No ions

   Initial geometry:
   - base_model_incl_N185eh.lipids_protein_glycans.initial_geometry.psf
   - base_model_incl_N185eh.lipids_protein_glycans.initial_geometry.pdb

   Equilibrated structure:
   - base_model_incl_N185eh.lipids_protein_glycans.equilibrated.psf
   - base_model_incl_N185eh.lipids_protein_glycans.equilibrated.pdb
   
   Final structure after MD (5 frames, one from each replica):
   - base_model_incl_N185eh.lipids_protein_glycans.final_all.pdb

B) protein_glycans_only
   Includes:
   - Protein
   - Glycans
   - No lipids
   - No water
   - No ions

   Initial geometry:
   - base_model_incl_N185eh.protein_glycans_only.initial_geometry.psf
   - base_model_incl_N185eh.protein_glycans_only.initial_geometry.pdb

   Equilibrated structure:
   - base_model_incl_N185eh.protein_glycans_only.equilibrated.psf
   - base_model_incl_N185eh.protein_glycans_only.equilibrated.pdb

   This reduced system is provided for simplified visualization
   (e.g., Chimera compatibility) and analyses focused only on
   protein and glycan components.


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RECOMMENDED USAGE (VMD)
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To visualize only the initial geometry structure including lipids:

1) Load the equilibrated PSF:
   mol new base_model_incl_N185eh.lipids_protein_glycans.initial_geometry.psf

2) Load PDB:
   mol addfile base_model_incl_N185eh.lipids_protein_glycans.initial_geometry.pdb waitfor all

NOTE:
Always load the PSF file first, followed by the PDB or DCD,
to ensure correct bonding and topology representation.
