The document discusses different molecular file formats and conversion tools. The two main molecular file formats are PDB and CHARMM, with PDB containing title, remarks, structure, and other sections and CHARMM used for molecular mechanisms, dynamics, analysis, and quantum/mechanics calculations. Conversion tools like Pdb2cif, Cif2pdb, Babel, Into Cham, and Mol2Mol are used to interconvert between different file formats, with Babel assigning properties and Mol2Mol supporting over 50 formats.

2. MOLECULAR FILE FORMATS
The two mostly used molecular file formats are as follows:
PDB File format
CHARMm file format
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3. SECTIONS AND RECORDS IN PDB FILE FORMAT
Title section
Remarks section
Primary structure section
Heterogenic section
Secondary structure section
Connectivity/annotation section
Miscellaneous feature section
Crystallographic and coordinate transformation section
coordinate transformation section
Coordinate section
Connectivity section
Bookkeeping section
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4. CHARMM FILE FORMAT
Molecular mechanisms and molecular dynamics software
Empirical potential energy function
Energy minimization
Molecular dynamics simulation
Vibrational analysis
Thermodynamic analysis
Quantum mechanics and molecular mechanics calculation
Title line begins with a * and also in the next line ends with a
*

5. MOLECULAR CONVERSION TOOLS
Pdb2cif
Cif2pdb
Babel
Into Cham
Mol2Mol
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6. BABEL
Interconverts number of molecular file formats
Used in molecular modeling
Assigning hybridization
Bond order
Connectivity in the input file when its not already present

7. MOL2MOL
File formats inter-conversion
Reads about 50 file formats and sub formats

8. THANKS
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