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Generate MD topologies for small molecules (version 21.10+galaxy0)
Structure of the compound in pdb or mol2 format
Default value is 1, which is correct for almost all organic molecules.
Save atomic coordinates of ligand in GRO format.

Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools.


Either a mol2 file (more appropriate for small structures) or a pdb file. If you want to parameterize a large macromolecule (which is more likely to be stored in PDB format, e.g. a protein) consider using a tool such as 'GROMACS initial setup' instead.


GROMACS topology for the ligand, in itp format. Optional: structure file, in gro format.