Helper applications

Volume guesser: Given the number of molecules of each type, their molar mass and the desired density, estimates the total volume of the system. Online. [Click here] solvate.tcl: With a single command solvates a protein with water and ions in a rectangular box. Distributed alongside with the packmol package. maxmin.tcl Gets the maximum and minimum coordinates of the atoms of a PDB file (or of selected atoms). TCL script. [Click here] charge.tcl Reads a PDB file and computes the total charge of protein molecules in it, considering standard protonation states. Outputs the number of charged residues of each type and histidines. TCL script. [Click here] molarmass.tcl Reads a PDB file and computes the molar mass of some selected group of atoms. TCL script. [Click here] addter.tcl Add the "TER" word between different molecules in a file generated with multiple molecules. This is required by AMBER, so it may be useful. TCL script. [Click here] This can be done automatically with packmol, by adding the "add_amber_ter" option to the input file.

User provided

Cellulose Builder Creating crystalline materials is not a Packmol task and can be tricky. This package build cellulose fibers in crystalline forms with user determined sizes and geometries, which can then be solvated with Packmol. [Home-Page] Avogadro's packmol plugin Tim Vandermeersch is developing a beautiful Packmol plugin for Avogadro, consisting of a user interface that will help many people to use Packmol. This looks very promising, and we are following closely its development! More at Tim's blog and at the project's source repository. MolecV1 Iteratively asks properties of the system, as the density and type of box to be created, and writes a input file for packmol. [Click here]