PACKMOL

Initial configurations for Molecular Dynamics Simulations by packing optimization

Institute of Chemistry and Institute of Mathematics
University of Campinas
Institute of Mathematics and Statistics
University of São Paulo

Packmol:

Download
Input Examples
User guide
Utilities
External links
Applications

Reference:

Citation
Features
Version history

Contact:

E-mail
Regular mail

Helper applications

Some applications that can help you to determinte the geometrical properties of the system, its charge, and its density.

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.