Mod:Hunt Research Group/Chemshell:Chemshell: QM/MM Single Point and optimisation inputs
Choose a name for each file and then insert it where needed in the .py file.
The .pun file:
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
The .ff file:
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
The .py file:
'''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