API Documentation

autosolvate.startboxgen(argumentList)

Wrap function that parses command line options for autosolvate boxgen, adds solvent box to a given solute, and generates related force field parameters.

autosolvate.solventBoxBuilder(xyzfile[, ...])

Solvated molecule in specified solvent.

autosolvate.solventBoxBuilder.build()

Run solventBoxBuilder

autosolvate.solventBoxBuilder.getSolutePDB()

Convert xyz to pdb

autosolvate.solventBoxBuilder.getFrcmod()

Get partial charges and create frcmod

autosolvate.solventBoxBuilder.getHeadTail()

Detect start and end of coordinates

autosolvate.solventBoxBuilder.writeTleapcmd1()

Create tleap input file

autosolvate.solventBoxBuilder.createLib()

Run tleap

autosolvate.solventBoxBuilder.writeTleapcmd_add_solvent()

Write tleap input file to add solvent

autosolvate.solventBoxBuilder.processPackmolPDB()

Convert file for custom solvents like CH3CN

autosolvate.solventBoxBuilder.packSLUSLV()

Write packmol input file for custom solvents

autosolvate.solventBoxBuilder.writeTleapcmd_custom_solvated()

Write tleap file for custom solvents like CH3CN

autosolvate.solventBoxBuilder.createAmberParm()

Generate Amber parameters with tleap

autosolvate.generatetrajs.startmd(argumentList)

Wrap function that parses command line options for autosolvate clustergen, generates inputfiles for Amber and TeraChem, runs MM and QMMM stages.

autosolvate.generatetrajs.writeMMminInput([...])

Write Amber MM minimization input file

autosolvate.generatetrajs.writeMMheatInput([...])

Write Amber MM heating input file

autosolvate.generatetrajs.writeMMNVEInput([...])

Write Amber MM NVE input file

autosolvate.generatetrajs.writeMMNPTInput([...])

Write Amber MM NPT input file

autosolvate.generatetrajs.runMM([filename, ...])

Equilibrate with MM

autosolvate.generatetrajs.writeQMMMTemplate([...])

Write Terachem file-based interface to Amber

autosolvate.generatetrajs.writeQMMMMinInput([...])

Write QMMM min input file

autosolvate.generatetrajs.writeQMMMInput([...])

Write QMMM heating or NPT trajectory input file

autosolvate.generatetrajs.runQMMM([...])

Run QMMM minimization, heating and NVT trajectory run

autosolvate.clustergen.clustergen([...])

Extract microsolvated cluster around center solute

autosolvate.clustergen.startclustergen(...)

Wrap function that parses command line options for autosolvate clustergen, extracts microsolvated clusters from trajectory,