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
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See also:
The TANGO project
MDLovoFit
LovoAlign
LM Home-Page
JM Home-Page
EGB Home-Page
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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.