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The structure mapping tool allows one to map an atomistic representation of a single molecule to a coarse-grained representation.

The end result is a topology and weights mapping XML file as is used in VOTCA or DL CGMAP coarse-graining packages.

STOCK: Structure mapping tool

structure mapper and online coarse-graining kit

Molecule
Weights
Beads
Bonds
Angles
Dihedrals
XML
Custom

...

Molecule name:
Molecule ident:

Weight name:
Weights:
Automatically map weights

Bead name:
Bead type:
Map weights:
Group select

Bead size:

Bond name:
With beads:

Angle name:
With beads:

Dihedral name:
With beads:

show labels hide beads hide atoms black reset view

If you use this tool, please cite:
S. Bevc, C. Junghans, M. Praprotnik (2015) STOCK: Structure mapper and online coarse-graining kit for molecular simulations. Journal of Computational Chemistry, 36, 467, doi: 10.1002/jcc.23806 (Link, BibteX)