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Generate MD topologies for small molecules (version 21.10+galaxy0)

Input file:

Structure of the compound in pdb or mol2 format

Charge of the molecule:

Multiplicity:

Default value is 1, which is correct for almost all organic molecules.

Force field to use for parameterization:

Charge method:

Save GRO file?:

Save atomic coordinates of ligand in GRO format.

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

Input

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.

Outputs

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