top.top

;
;   File top.top  was generated
;   By user: parashara (501)
;   On host: Parasharas-MacBook-Pro.local
;   At date: Wed. February  3 12:57:49 2020
;
;   This is a standalone topology file
;
;   Created by:
;   ParmEd:       test.py, VERSION 3.2.0
;   Executable:   test.py
;   Library dir:  /Users/parashara/Documents/devel/src/gromacs/install/share/gromacs/top
;   Command line:
;     test.py
;

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               3               yes             1            1           

[ atomtypes ]
; name    at.num    mass    charge ptype  sigma      epsilon
CH4            0  16.043000  0.00000000  A          0.373        1.23054
CH3            0  15.035000  0.00000000  A          0.375       0.814817
OH             0  15.999400  0.00000000  A          0.302       0.773245


[ moleculetype ]
; Name            nrexcl
RES          3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr    charge       mass  typeB    chargeB      massB
; residue    1 RES rtp RES q 0.0
    1        CH4      1    RES   _CH4      1 0.00000000  16.043000   ; qtot 0.000000

[ system ]
; Name
Generic title

[ molecules ]
; Compound       #mols
RES                 16

topology_pr121_ua_test.py

import mbuild as mb
from foyer import Forcefield
import topology
from topology.external.convert_parmed import from_parmed
from topology.formats.top import write_top
from topology.formats.gro import write_gro

methane_cmpd = mb.Compound()
methane_particle = mb.Particle(name="_CH4")
methane_cmpd.add(methane_particle)
methanol = mb.Compound()
ch3 = mb.Particle(name="_CH3")
oh = mb.Particle(name="_OH")
methanol.add([ch3, oh])

ch3_port = mb.Port(anchor=ch3, orientation=[1,0,0], separation=0.07)
methanol.add(ch3_port, label='right')

oh_port = mb.Port(anchor=oh, orientation=[-1,0,0], separation=0.07)
methanol.add(oh_port, label='left')

mb.force_overlap(move_this=oh,
                from_positions=methanol['left'],
                to_positions=methanol['right'])

methane_grid = mb.Grid3DPattern(2,2,2)
methane_grid.scale(0.4)
list_of_methanes = methane_grid.apply(methane_cmpd)
methane_box = mb.Compound(list_of_methanes)

methanol_grid = mb.Grid3DPattern(2,2,2)
methanol_grid.scale(0.4)
list_of_methanols = methane_grid.apply(methanol)
methanol_box = mb.Compound(list_of_methanols)

methanol_box.translate([0,0, 1.1*max(methane_box.xyz[:,2])])

mixture_box = mb.Compound([methane_box, methanol_box])

ff = Forcefield(forcefield_files='ff.xml')
struc = ff.apply(mixture_box)

top = from_parmed(struc)
write_top(top, "test.top")
write_gro(top, "test.gro")