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The .pun file:

<pre>
block = fragment records = 0
block = title records = 1
    Built with Packmol
block = coordinates records = 70
CA 3.80212868902079e+001 4.65080463049159e+001 6.27181158349459e+001 
HA 3.70348499241697e+001 4.51039798954017e+001 6.38973048518191e+001 
HA 3.79816026444478e+001 4.80991955872993e+001 6.38651795100133e+001 
HA 3.70046143083525e+001 4.66289887681849e+001 6.09209864198073e+001 
CA 4.09541416244824e+001 4.30989806215195e+001 6.15842802417985e+001 
HA 4.01585669832907e+001 4.27248148757809e+001 5.97512460328770e+001 
HA 4.29874867881934e+001 4.27890655593926e+001 6.14822350384153e+001 
HA 4.00659704098503e+001 4.16646785961881e+001 6.28938603518837e+001 
CA 4.20936463955955e+001 4.61489983670859e+001 6.48043733263370e+001 
HA 4.15720820227477e+001 4.46050922344169e+001 6.60931664505478e+001 
HA 4.42743901864156e+001 4.61678956269717e+001 6.47042178489423e+001 
HA 4.14832649012845e+001 4.80462832596191e+001 6.55829404336315e+001 
CS 4.17232601018341e+001 4.76947942257435e+001 6.04939083463885e+001 
HS 4.08502066951106e+001 4.74226736833881e+001 5.87194556431129e+001 
HS 4.38397532090424e+001 4.74585784771711e+001 6.03087151995078e+001 
NA 4.07613895736474e+001 4.58107374151303e+001 6.23666268010702e+001 
CW 4.15626333928048e+001 5.06333181379837e+001 6.09909062813847e+001 
HW 4.24281278955740e+001 5.10963010051855e+001 6.28390582982149e+001 
HW 3.95973183646828e+001 5.11964564825802e+001 6.13405055892719e+001 
OY 4.26643436441464e+001 5.19844722198176e+001 5.89613405696510e+001 
HY 4.14152347656957e+001 5.29066585022441e+001 5.81241919567105e+001 
CA 4.27966244633469e+001 5.36568797197099e+001 7.32986916449993e+001 
HA 4.42895079943242e+001 5.26912297395461e+001 7.43607176505806e+001 
HA 4.35695223926757e+001 5.40763988891745e+001 7.14694368880549e+001 
HA 4.22202580368303e+001 5.54615680388028e+001 7.43550484726149e+001 
CA 3.94215738477449e+001 5.11662208667629e+001 7.51676306477038e+001 
HA 3.90511875539834e+001 5.25967434401172e+001 7.65112258255835e+001 
HA 3.77075923761038e+001 5.01136434911245e+001 7.49862169528002e+001 
HA 4.08672142290078e+001 4.97527058273059e+001 7.58762778934209e+001 
CA 4.13585429860383e+001 4.97867208951003e+001 7.13031410010599e+001 
HA 4.27701682995068e+001 4.85527298245583e+001 7.20835978343430e+001 
HA 3.98410930172094e+001 4.85319428386839e+001 7.09932259389330e+001 
HA 4.20275059859953e+001 5.03668667735940e+001 6.95060115859214e+001 
CS 3.85541896189872e+001 5.35416064344066e+001 7.12426697694254e+001 
HS 3.81214423676026e+001 5.53633022873967e+001 7.21932019416806e+001 
HS 3.68761129411291e+001 5.25759564542428e+001 7.14448704502034e+001 
NA 4.05384019069951e+001 5.20713996152922e+001 7.27695683681972e+001 
CW 3.91985861810926e+001 5.42237975162836e+001 6.85479205097119e+001 
HW 3.93951176839048e+001 5.24946982367339e+001 6.74821150521534e+001 
HW 4.07122566979443e+001 5.56051872139348e+001 6.84780006481345e+001 
OY 3.70858725258614e+001 5.52121242083104e+001 6.72874732753297e+001 
HY 3.72616170427992e+001 5.68826419822142e+001 6.66695328770644e+001 
Cl 4.60488428896912e+001 5.15044818187186e+001 6.55489253658371e+001 
C 4.78743181946584e+001 4.32860634943888e+001 6.72629068374782e+001 
N 4.95183798047221e+001 4.35525148587784e+001 6.53656219449450e+001 
O 4.67310339715682e+001 4.13150792883010e+001 6.77277794306686e+001 
N 4.74359017653081e+001 4.54422408473574e+001 6.86027225633807e+001 
HT 4.83618674997118e+001 4.70938613613753e+001 6.81661958600189e+001 
HC 4.60941963134171e+001 4.55461757767292e+001 7.00219067808034e+001 
HT 5.04216688272628e+001 4.52457093445452e+001 6.53410555070934e+001 
HC 4.97016832256143e+001 4.21843532430473e+001 6.40201370410768e+001 
C 5.19088831802745e+001 4.96979037736371e+001 6.13216083293861e+001 
N 5.20354948215092e+001 5.03366311577768e+001 6.37499062247100e+001 
O 5.38061680728077e+001 4.92216928245152e+001 6.00422638351181e+001 
N 4.96733373357856e+001 4.98301845928376e+001 6.03049357475306e+001 
HT 4.80009298358932e+001 5.04462352651144e+001 6.12063350440828e+001 
HC 4.94446804911675e+001 4.93331866578414e+001 5.85210344143121e+001 
HT 5.04178893752857e+001 5.09167770362705e+001 6.47798068884855e+001 
HC 5.37494762931503e+001 5.02137989685191e+001 6.46305185353878e+001 
C 5.01854530786905e+001 5.89273255018566e+001 6.69926760211114e+001 
N 5.02572626662565e+001 5.64857995246126e+001 6.66770917810187e+001 
O 5.21167530390181e+001 6.00460432870953e+001 6.76370725832168e+001 
N 4.79215613443729e+001 6.00554919170382e+001 6.72307814956723e+001 
HT 4.63417504179209e+001 5.90104734453540e+001 6.70021246510543e+001 
HC 4.79706942200760e+001 6.18507316061882e+001 6.76257342272853e+001 
HT 4.87076873556217e+001 5.54426707789170e+001 6.64881191821608e+001 
HC 5.18748681124800e+001 5.54483399568828e+001 6.69359842414540e+001 
OU 4.84053311974491e+001 5.24209989231793e+001 7.08307095039152e+001 
HU 4.78232955929668e+001 5.21526578328011e+001 6.91394047441371e+001 
HU 4.99662448640153e+001 5.15082612706957e+001 7.09233060773556e+001 
block = connectivity records = 0
</pre>

The .ff file: 

<pre>
ChCl:Urea + TIP4P2005 Water with forcefield of Doherty et al. JPCB 122, 9982 (2018)
UNITS kcal/mol

molecules 2
Choline
nummols     2
atoms 21
CA        12.0107      -0.100      1
HA        1.00794       0.033      3
CA        12.0107      -0.100      1
HA        1.00794       0.033      3
CA        12.0107      -0.100      1
HA        1.00794       0.033      3
CS        12.0107      -0.131      1
HS        1.00794       0.068      2
NA        14.0067       0.791      1
CW        12.0107       0.132      1
HW        1.00794       0.034      2
OY        15.9994      -0.468      1
HY        1.00794       0.275      1
bonds   20
harm    1    2   680.0  1.099  0.0 0.0  # CA-HA
harm    1    3   680.0  1.099  0.0 0.0  # CA-HA
harm    1    4   680.0  1.099  0.0 0.0  # CA-HA
harm    1   16   980.0  1.498  0.0 0.0  # CA-NA
harm    5    6   680.0  1.099  0.0 0.0  # CA-HA
harm    5    7   680.0  1.099  0.0 0.0  # CA-HA
harm    5    8   680.0  1.099  0.0 0.0  # CA-HA
harm    5   16   980.0  1.498  0.0 0.0  # CA-NA
harm    9   10   680.0  1.099  0.0 0.0  # CA-HA
harm    9   11   680.0  1.099  0.0 0.0  # CA-HA
harm    9   12   680.0  1.099  0.0 0.0  # CA-HA
harm    9   16   980.0  1.498  0.0 0.0  # CA-NA
harm   13   16   980.0  1.516  0.0 0.0  # CS-NA
harm   13   14   680.0  1.0805 0.0 0.0  # CS-HS
harm   13   15   680.0  1.0805 0.0 0.0  # CS-HS
harm   13   17   634.0  1.521  0.0 0.0  # CS-CW
harm   17   18   680.0  1.085  0.0 0.0  # CW-HW
harm   17   19   680.0  1.085  0.0 0.0  # CW-HW
harm   17   20   900.0  1.395  0.0 0.0  # CW-OY
harm   20   21  1106.0  0.949  0.0 0.0  # OY-HY
angles 37
harm     8    5    6   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm     8    5    7   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm     6    5    7   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm     2    1    3   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm     2    1    4   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm     3    1    4   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm    12    9   10   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm    12    9   11   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm    10    9   11   70.0   110.01  0.0 0.0 0.0 0.0   #  HA-CA-HA
harm     8    5   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm     6    5   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm     7    5   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm     2    1   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm     3    1   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm     4    1   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm    12    9   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm    10    9   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm    11    9   16   70.0   108.90  0.0 0.0 0.0 0.0   #  HA-CA-NA
harm     5   16   13  103.6   110.20  0.0 0.0 0.0 0.0   #  CA-NA-CS
harm     1   16   13  103.6   110.20  0.0 0.0 0.0 0.0   #  CA-NA-CS
harm     9   16   13  103.6   110.20  0.0 0.0 0.0 0.0   #  CA-NA-CS
harm    16   13   14   70.0   106.40  0.0 0.0 0.0 0.0   #  NA-CS-HS
harm    16   13   15   70.0   106.40  0.0 0.0 0.0 0.0   #  NA-CS-HS
harm    16   13   17  140.0   116.60  0.0 0.0 0.0 0.0   #  NA-CS-CW
harm    13   17   18   70.0   108.30  0.0 0.0 0.0 0.0   #  CS-CW-HW
harm    13   17   19   70.0   108.30  0.0 0.0 0.0 0.0   #  CS-CW-HW
harm    13   17   20  160.0   109.60  0.0 0.0 0.0 0.0   #  CS-CW-OY
harm    14   13   17   70.0   109.30  0.0 0.0 0.0 0.0   #  HS-CS-CW
harm    15   13   17   70.0   109.30  0.0 0.0 0.0 0.0   #  HS-CS-CW
harm    18   17   20   70.0   111.60  0.0 0.0 0.0 0.0   #  HW-CW-OY
harm    19   17   20   70.0   111.60  0.0 0.0 0.0 0.0   #  HW-CW-OY
harm    17   20   21   70.0   110.90  0.0 0.0 0.0 0.0   #  CW-OY-HY
harm     5   16    1  110.0   108.73  0.0 0.0 0.0 0.0   #  CA-NA-CA
harm     5   16    9  110.0   108.73  0.0 0.0 0.0 0.0   #  CA-NA-CA
harm     1   16    9  110.0   108.73  0.0 0.0 0.0 0.0   #  CA-NA-CA
harm    14   13   15   70.0   108.60  0.0 0.0 0.0 0.0   #  HS-CS-HS
harm    18   17   19   70.0   107.40  0.0 0.0 0.0 0.0   #  HW-CW-Hw
dihedrals 52
cos3    17   13  16   5   0.100   0.550   0.650   0.5 0.5 0.0 0.0  # CW-CS-NA-CA
cos3    17   13  16   1   0.100   0.550   0.650   0.5 0.5 0.0 0.0  # CW-CS-NA-CA
cos3    17   13  16   9   0.100   0.550   0.650   0.5 0.5 0.0 0.0  # CW-CS-NA-CA
cos3     5   16   1   2   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     5   16   1   3   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     5   16   1   4   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     5   16   9  12   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     5   16   9  10   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     5   16   9  11   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     1   16   5   8   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     1   16   5   6   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     1   16   5   7   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     1   16   9  12   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     1   16   9  10   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     1   16   9  11   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     9   16   5   8   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     9   16   5   6   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     9   16   5   7   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     9   16   1   2   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     9   16   1   3   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3     9   16   1   4   0.000   0.000   0.825   0.5 0.5 0.0 0.0  # CA-NA-CA-HA
cos3    13   16   5   8   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   5   6   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   5   7   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   1   2   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   1   3   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   1   4   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   9  12   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   9  10   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    13   16   9  11   0.000   0.000   0.940   0.5 0.5 0.0 0.0  # CS-NA-CA-HA
cos3    14   13  16   5   0.000   1.000   0.700   0.5 0.5 0.0 0.0  # HS-CS-NA-CA
cos3    14   13  16   1   0.000   1.000   0.700   0.5 0.5 0.0 0.0  # HS-CS-NA-CA
cos3    14   13  16   9   0.000   1.000   0.700   0.5 0.5 0.0 0.0  # HS-CS-NA-CA
cos3    15   13  16   5   0.000   1.000   0.700   0.5 0.5 0.0 0.0  # HS-CS-NA-CA
cos3    15   13  16   1   0.000   1.000   0.700   0.5 0.5 0.0 0.0  # HS-CS-NA-CA
cos3    15   13  16   9   0.000   1.000   0.700   0.5 0.5 0.0 0.0  # HS-CS-NA-CA
cos3    20   17  13  16  -6.000  -5.000   3.200   0.5 0.5 0.0 0.0  # OY-CW-CS-NA
cos3    20   17  13  14  -0.500  -2.500   0.250   0.5 0.5 0.0 0.0  # OY-CW-CS-HS
cos3    20   17  13  15  -0.500  -2.500   0.250   0.5 0.5 0.0 0.0  # OY-CW-CS-HS
cos3    18   17  13  16  -6.000  -7.000   0.750   0.5 0.5 0.0 0.0  # HW-CW-CS-NA
cos3    19   17  13  16  -6.000  -7.000   0.750   0.5 0.5 0.0 0.0  # HW-CW-CS-NA
cos3    18   17  13  14   6.000  -3.000   2.000   0.5 0.5 0.0 0.0  # HW-CW-CS-HS
cos3    18   17  13  15   6.000  -3.000   2.000   0.5 0.5 0.0 0.0  # HW-CW-CS-HS
cos3    19   17  13  14   6.000  -3.000   2.000   0.5 0.5 0.0 0.0  # HW-CW-CS-HS
cos3    19   17  13  15   6.000  -3.000   2.000   0.5 0.5 0.0 0.0  # HW-CW-CS-HS
cos3    21   20  17  13  -0.356  -0.174   0.350   0.5 0.5 0.0 0.0  # HY-OY-CW-CS
cos3    21   20  17  18  -3.000   1.000  -2.000   0.5 0.5 0.0 0.0  # HY-OY-CW-HW
cos3    21   20  17  19  -3.000   1.000  -2.000   0.5 0.5 0.0 0.0  # HY-OY-CW-HW
cos3     5   16   1   9   0.000   2.000   0.000   0.5 0.5 0.0 0.0  # CA-NA-CA-CA improper
cos3    13   16   5   1   0.000   2.000   0.000   0.5 0.5 0.0 0.0  # CS-NA-CA-CA improper
cos3    13   16   5   9   0.000   2.000   0.000   0.5 0.5 0.0 0.0  # CS-NA-CA-CA improper
cos3    13   16   1   9   0.000   2.000   0.000   0.5 0.5 0.0 0.0  # CS-NA-CA-CA improper
finish
Urea
nummols      3
atoms 8
C         12.0107       0.124      1
N         14.0067      -0.453      1
O         15.9994      -0.322      1
N         14.0067      -0.453      1
HT        1.00794       0.276      1
HC        1.00794       0.276      1
HT        1.00794       0.276      1
HC        1.00794       0.276      1
bonds      7
harm    1    2   980.0  1.335  0.0 0.0  # C-N
harm    1    3  1140.0  1.229  0.0 0.0  # C-O
harm    1    4   980.0  1.335  0.0 0.0  # C-N
harm    2    7   868.0  1.010  0.0 0.0  # N-HT
harm    2    8   868.0  1.010  0.0 0.0  # N-HC
harm    4    5   868.0  1.010  0.0 0.0  # N-HT
harm    4    6   868.0  1.010  0.0 0.0  # N-HC
angles     9
harm    2    1    3  160.0  122.90 0.0 0.0 0.0 0.0  # N-C-O
harm    2    1    4  140.0  114.20 0.0 0.0 0.0 0.0  # N-C-N
harm    4    1    3  160.0  122.90 0.0 0.0 0.0 0.0  # N-C-O
harm    1    2    7   70.0  119.80 0.0 0.0 0.0 0.0  # C-N-HT
harm    1    2    8   70.0  119.80 0.0 0.0 0.0 0.0  # C-N-HC
harm    1    4    5   70.0  119.80 0.0 0.0 0.0 0.0  # C-N-HT
harm    1    4    6   70.0  119.80 0.0 0.0 0.0 0.0  # C-N-HC
harm    5    4    6   70.0  120.00 0.0 0.0 0.0 0.0  # HT-N-HC
harm    7    2    8   70.0  120.00 0.0 0.0 0.0 0.0  # HT-N-HC
dihedrals 11
cos3    3    1    2    7   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    3    1    2    8   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    3    1    4    5   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    3    1    4    6   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    4    1    2    7   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    4    1    2    8   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    2    1    4    5   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    2    1    4    6   0.0000    4.9000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-HT
cos3    7    2    1    8   0.0000    5.0000   0.0000  0.5 0.5 0.0 0.0  # HT-N-C-HC improper
cos3    5    4    1    6   0.0000    5.0000   0.0000  0.5 0.5 0.0 0.0  # HT-N-C-HC improper
cos3    3    1    2    4   0.0000   21.0000   0.0000  0.5 0.5 0.0 0.0  # O-C-N-N   improper
finish
vdw  66
CS      CS        LJ      0.06600     3.50000
CS      HS        LJ      0.04450     3.01662
CS      NA        LJ      0.10592     3.37268
CS      CA        LJ      0.06600     3.50000
CS      CW        LJ      0.06600     3.50000
CS      OY        LJ      0.10592     3.27796
CS      HA        LJ      0.04450     2.95804
CS      HW        LJ      0.04450     2.77489
CS      C         LJ      0.10196     3.62284
CS      O         LJ      0.14419     3.21870
CS      N         LJ      0.12973     3.52491
HS      HS        LJ      0.03000     2.60000
HS      NA        LJ      0.07141     2.90689
HS      CA        LJ      0.04450     3.01662
HS      CW        LJ      0.04450     3.01662
HS      OY        LJ      0.07141     2.82524
HS      HA        LJ      0.03000     2.54951
HS      HW        LJ      0.03000     2.39165
HS      C         LJ      0.06874     3.12250
HS      O         LJ      0.09721     2.77417
HS      N         LJ      0.08746     3.03809
NA      NA        LJ      0.17000     3.25000
NA      CA        LJ      0.10592     3.37268
NA      CW        LJ      0.10592     3.37268
NA      OY        LJ      0.17000     3.15872
NA      HA        LJ      0.07141     2.85044
NA      HW        LJ      0.07141     2.67395
NA      C         LJ      0.16363     3.49106
NA      O         LJ      0.23141     3.10161
NA      N         LJ      0.20821     3.39669
CA      CA        LJ      0.06600     3.50000
CA      CW        LJ      0.06600     3.50000
CA      OY        LJ      0.10592     3.27796
CA      HA        LJ      0.04450     2.95804
CA      HW        LJ      0.04450     2.77489
CA      C         LJ      0.10196     3.62284
CA      O         LJ      0.14419     3.21870
CA      N         LJ      0.12973     3.52491
CW      CW        LJ      0.06600     3.50000
CW      OY        LJ      0.10592     3.27796
CW      HA        LJ      0.04450     2.95804
CW      HW        LJ      0.04450     2.77489
CW      C         LJ      0.10196     3.62284
CW      O         LJ      0.14419     3.21870
CW      N         LJ      0.12973     3.52491
OY      OY        LJ      0.17000     3.07000
OY      HA        LJ      0.07141     2.77038
OY      HW        LJ      0.07141     2.59885
OY      C         LJ      0.16363     3.39301
OY      O         LJ      0.23141     3.01450
OY      N         LJ      0.20821     3.30129
HA      HA        LJ      0.03000     2.50000
HA      HW        LJ      0.03000     2.34521
HA      C         LJ      0.06874     3.06186
HA      O         LJ      0.09721     2.72029
HA      N         LJ      0.08746     2.97909
HW      HW        LJ      0.03000     2.20000
HW      C         LJ      0.06874     2.87228
HW      O         LJ      0.09721     2.55186
HW      N         LJ      0.08746     2.79464
C       C         LJ      0.15750     3.75000
C       O         LJ      0.22274     3.33167
C       N         LJ      0.20041     3.64863
O       O         LJ      0.31500     2.96000
O       N         LJ      0.28342     3.24160
N       N         LJ      0.25500     3.55000
close
</pre>

The .py file:

<pre>
'''Choline Chloride / Urea / water 0.8'''

from chemsh       import *

cluster = Fragment(coords='<name of .pun file>.pun', connmode=None)



qm = NWChem(method="hf", basis="3-21g", charge=-1)
mm = DL_POLY(ff='<name of .ff file>.ff', temperature=0.0)

qmmm = QMMM(frag=cluster, qm_region=[42,67,68,69], qm=qm, mm=mm, embedding='electrostatic', coupling='covalent')

print("### qmmm.qm_region =", qmmm.qm_region)
print("### qmmm.mm_region =", qmmm.mm_region)
print("### qmmm.mm.qmatoms =", qmmm.mm.qmatoms)
print("### qmmm.mm.mmatoms =", qmmm.mm.mmatoms)
print("### qmmm.mm.frag.names =", qmmm.qm.frag.natoms, qmmm.mm.frag.natoms)

#opt = Opt(active=[42, 67, 68, 69], theory=qmmm, maxcycle=100)
sp = SP(theory=qmmm, gradients=True)

#opt.run()
sp.run()


ecalc = sp.result.energyecalc = sp.result.energy
</pre>