Generate Gromacs Topology File

Classes

class gentop.SystemTopology(gro, ff='gaff', restraints=False, xlink=False, xlinked_top_name='assembly.itp', fix_residues=False)

__init__(gro, ff='gaff', restraints=False, xlink=False, xlinked_top_name='assembly.itp', fix_residues=False)

Read coordinate file, identify and count different residues, and figure out where inidividual residue topologies are located

Parameters:

• gro (str) – coordinate file for which to create topology
• ff (str) – forcefield to use
• restraints (bool) – True if there are any position restraints
• xlink (bool) – True if system is cross-linked (Topology is specialized in this case)
• xlinked_top_name (str) – Name of topology describing cross-linked system (include full path if not located in same directory where this script is run)

add_residue(residue, n=1, write=False, topname='topol.top', top_description='Simulation Box')

Add molecule(s) of a single residue to the topology

Parameters:

• residue (LLC_Membranes.llclib.topology.Residue object) – name of residue object
• n (int) – number of molecules to add
• write (bool) – write new topology file
• topname (str) – name of output topology if written
• top_description (str) – system description to be written into top if desired

remove_residue(residue, n=1, write=False, topname='topol.top', top_description='Simulation Box')

Remove a residue from the topology

Parameters:

• residue (LLC_Membranes.llclib.topology.Residue object) – name of residue object
• n (int) – number of molecules to add
• write (bool) – write new topology file
• topname (str) – name of output topology if written
• top_description (str) – system description to be written into top if desired

write_top(name='topol.top', description='Simulation Box', restrained_top_name='restrained.itp')

Write out the topology in appropriate GROMACS format

Parameters:

• name (str) – name of output topology file
• description (str) – Description to add to [ system ] section of topology
• restrained_top_name (str) – Name of topology file that includes position restraints (TODO: add this to __init__)

Command Line Functionality

One can run this as a script from the command line as follows. However, in most cases it is probably more convenient to use input.py

Generate topology file from coordinate file.

usage: gentop.py [-h] [-g GRO] [-o OUTPUT] [-d DESCRIPTION] [-ff FORCEFIELD]
                 [-xlink] [-xlink_topname XLINK_TOPNAME]

Named Arguments

-g, --gro	Name of coordinate file to write topology file for
-o, --output	Name of topology to output Default: “topol.top”
-d, --description
	Description of system to put under [ system ] directive Default: “Simulation box”
-ff, --forcefield
	Name of forcefield to use Default: “gaff”
-xlink	Create topology for cross-linked system Default: False
-xlink_topname	Name of cross-linked topology Default: “assembly.itp”