API Documentation
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Wrap function that parses command line options for autosolvate boxgen, adds solvent box to a given solute, and generates related force field parameters. |
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Solvated molecule in specified solvent. |
Run solventBoxBuilder |
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Convert xyz to pdb |
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Get partial charges and create frcmod |
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Detect start and end of coordinates |
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Create tleap input file |
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Run tleap |
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Write tleap input file to add solvent |
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Convert file for custom solvents like CH3CN |
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Write packmol input file for custom solvents |
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Write tleap file for custom solvents like CH3CN |
Generate Amber parameters with tleap |
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Wrap function that parses command line options for autosolvate clustergen, generates inputfiles for Amber and TeraChem, runs MM and QMMM stages. |
Write Amber MM minimization input file |
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Write Amber MM heating input file |
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Write Amber MM NVE input file |
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Write Amber MM NPT input file |
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Equilibrate with MM |
Write Terachem file-based interface to Amber |
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Write QMMM min input file |
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Write QMMM heating or NPT trajectory input file |
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Run QMMM minimization, heating and NVT trajectory run |
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Extract microsolvated cluster around center solute |
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Wrap function that parses command line options for autosolvate clustergen, extracts microsolvated clusters from trajectory, |