Mod:Hunt Research Group/basiconiom
Basic ONIOM (Mechanical Embedding)
1. Sample ONIOM input file (e.g. toy.com)
%chk=toy.chk %mem=5800MB %nprocshared=4 #p opt=(calcfc,quadmacro) oniom(b3lyp/6-31+g(d,p):amber=(softonly,print)) nosymm geom=connectivity blank line Test Bisulfate and Water blank line -1 1 -1 1 -1 1 S-S-1.270000 0 0.10284895 0.02757327 0.05534583 H O-O1--0.640000 0 0.95090502 -1.05075883 -0.81085201 H O-O2--0.670000 0 -0.51087811 0.82245133 -0.91214172 H O-O3--0.670000 0 -0.81851250 -0.72427103 0.81164058 H O-O4--0.670000 0 1.11462042 0.79477780 0.80476499 H H-H-0.380000 0 0.45941997 -1.72717140 -1.30097755 H O-OW--0.847600 0 3.31669151 0.92337934 2.20457485 L H-HW-0.423800 0 2.45080557 0.82778355 1.63296313 L H-HW-0.423800 0 3.48603341 -0.04930496 2.47598596 L O-OW--0.847600 0 -0.22954592 2.02696219 2.80161775 L H-HW-0.423800 0 0.26747515 1.48301390 2.11598828 L H-HW-0.423800 0 0.28064120 1.84302227 3.63593862 L O-OW--0.847600 0 -2.29924951 -1.45878390 3.35153800 L H-HW-0.423800 0 -1.87326212 -1.03609584 2.58030291 L H-HW-0.423800 0 -2.87613390 -2.25478077 3.00874061 L O-OW--0.847600 0 -3.54879856 -0.88925095 0.08410237 L H-HW-0.423800 0 -3.87672866 -0.69332912 -0.88175409 L H-HW-0.423800 0 -2.59079526 -0.54744474 0.17954089 L O-OW--0.847600 0 -1.83913482 3.22538749 -0.59342039 L H-HW-0.423800 0 -1.29220416 2.34165819 -0.77772930 L H-HW-0.423800 0 -1.87947273 3.40788366 0.38849210 L O-OW--0.847600 0 -0.28045738 -3.12703664 -2.19490573 L H-HW-0.423800 0 0.08068071 -4.06820600 -2.35482136 L H-HW-0.423800 0 -1.31072517 -3.35441273 -2.29980667 L O-OW--0.847600 0 2.37543122 2.81921989 -1.66804655 L H-HW-0.423800 0 2.58818235 1.94618777 -1.18868481 L H-HW-0.423800 0 1.72881114 3.25739501 -1.07832183 L O-OW--0.847600 0 3.11591669 0.24299129 -1.58116804 L H-HW-0.423800 0 3.97376898 -0.23507194 -1.37416825 L H-HW-0.423800 0 2.39885963 -0.35034399 -1.06960474 L O-OW--0.847600 0 0.40050495 -3.04638717 1.40557679 L H-HW-0.423800 0 -0.10980106 -2.20999055 1.09766318 L H-HW-0.423800 0 0.81031776 -3.51765847 0.61371410 L O-OW--0.847600 0 -1.64745773 0.16003978 -3.18188232 L H-HW-0.423800 0 -1.23948138 0.44264616 -2.25324594 L H-HW-0.423800 0 -2.62310947 0.05217754 -2.86863471 L O-OW--0.847600 0 -5.08755345 1.49182027 1.58924908 L H-HW-0.423800 0 -5.05718425 0.81983890 2.36514831 L H-HW-0.423800 0 -5.16185625 0.85085664 0.81364159 L O-OW--0.847600 0 3.26723407 -4.03836556 -3.02872512 L H-HW-0.423800 0 4.19147258 -3.56273215 -3.22572177 L H-HW-0.423800 0 3.33695773 -5.00125243 -3.39061107 L O-OW--0.847600 0 -2.79617222 4.87207773 -2.64701036 L H-HW-0.423800 0 -2.38699550 4.19042036 -2.02914219 L H-HW-0.423800 0 -3.79636283 4.89932137 -2.44654765 L O-OW--0.847600 0 -3.79136740 -3.16014660 1.88872086 L H-HW-0.423800 0 -3.82220797 -2.37463058 1.22920675 L H-HW-0.423800 0 -4.72346956 -3.43258399 2.04504453 L O-OW--0.847600 0 -0.05332830 5.17293005 -2.62027162 L H-HW-0.423800 0 -1.04665234 5.08408816 -2.53325120 L H-HW-0.423800 0 0.26914823 4.46882731 -3.27838147 L O-OW--0.847600 0 1.96530067 -1.12975711 5.92766806 L H-HW-0.423800 0 2.13187580 -1.46550141 4.91366037 L H-HW-0.423800 0 1.03097963 -1.35565533 6.10178085 L O-OW--0.847600 0 4.87048460 1.41771674 -3.35630932 L H-HW-0.423800 0 5.43334848 1.87198187 -2.64889583 L H-HW-0.423800 0 4.02992477 1.02265590 -2.89918480 L O-OW--0.847600 0 -4.30979537 0.03115515 -2.36039196 L H-HW-0.423800 0 -4.94228341 0.87811472 -2.46496555 L H-HW-0.423800 0 -4.78898651 -0.75763020 -2.85020923 L O-OW--0.847600 0 5.35899322 -3.43204090 0.73861728 L H-HW-0.423800 0 4.79554562 -4.14684764 1.23026341 L H-HW-0.423800 0 6.04605274 -3.95498834 0.16323939 L O-OW--0.847600 0 3.16882416 3.14969257 4.25063400 L H-HW-0.423800 0 2.95532920 2.57234472 3.43529320 L H-HW-0.423800 0 3.04584297 4.14266981 3.91376106 L O-OW--0.847600 0 3.27948080 -5.16714298 1.69901926 L H-HW-0.423800 0 2.68631024 -4.74505979 0.98631060 L H-HW-0.423800 0 2.69838845 -5.95107243 2.06043996 L O-OW--0.847600 0 -1.23607274 2.60022378 -4.28824141 L H-HW-0.423800 0 -1.36968510 1.68064847 -3.90529225 L H-HW-0.423800 0 -0.21438016 2.78286215 -4.28590581 L O-OW--0.847600 0 1.36801994 3.39197449 -4.39578410 L H-HW-0.423800 0 1.89606292 3.44271062 -3.52170221 L H-HW-0.423800 0 2.01846091 3.30008448 -5.16935051 L O-OW--0.847600 0 1.61355606 -2.40592290 -3.98747917 L H-HW-0.423800 0 0.87336650 -2.63408396 -3.27166558 L H-HW-0.423800 0 2.40492124 -2.90639136 -3.61971395 L O-OW--0.847600 0 5.17914692 2.14279412 1.04921962 L H-HW-0.423800 0 4.51208728 1.55811859 1.69499597 L H-HW-0.423800 0 4.79453093 3.05702789 1.00916819 L O-OW--0.847600 0 -4.79851239 -0.03227942 3.70741132 L H-HW-0.423800 0 -4.73945444 0.27002293 4.68870800 L H-HW-0.423800 0 -3.90573817 -0.46172618 3.47416608 L O-OW--0.847600 0 -0.61933272 -2.71855519 5.89241093 L H-HW-0.423800 0 -0.72454676 -2.98041195 4.95310793 L H-HW-0.423800 0 -1.50983193 -2.27391277 6.06907574 L O-OW--0.847600 0 -2.61813265 2.99849925 2.41190720 L H-HW-0.423800 0 4.19147258 -3.56273215 -3.22572177 L H-HW-0.423800 0 3.33695773 -5.00125243 -3.39061107 L O-OW--0.847600 0 -2.79617222 4.87207773 -2.64701036 L H-HW-0.423800 0 -2.38699550 4.19042036 -2.02914219 L H-HW-0.423800 0 -3.79636283 4.89932137 -2.44654765 L O-OW--0.847600 0 -3.79136740 -3.16014660 1.88872086 L H-HW-0.423800 0 -3.82220797 -2.37463058 1.22920675 L H-HW-0.423800 0 -4.72346956 -3.43258399 2.04504453 L O-OW--0.847600 0 -0.05332830 5.17293005 -2.62027162 L H-HW-0.423800 0 -1.04665234 5.08408816 -2.53325120 L H-HW-0.423800 0 0.26914823 4.46882731 -3.27838147 L O-OW--0.847600 0 1.96530067 -1.12975711 5.92766806 L H-HW-0.423800 0 2.13187580 -1.46550141 4.91366037 L H-HW-0.423800 0 1.03097963 -1.35565533 6.10178085 L O-OW--0.847600 0 4.87048460 1.41771674 -3.35630932 L H-HW-0.423800 0 5.43334848 1.87198187 -2.64889583 L H-HW-0.423800 0 4.02992477 1.02265590 -2.89918480 L O-OW--0.847600 0 -4.30979537 0.03115515 -2.36039196 L H-HW-0.423800 0 -4.94228341 0.87811472 -2.46496555 L H-HW-0.423800 0 -4.78898651 -0.75763020 -2.85020923 L O-OW--0.847600 0 5.35899322 -3.43204090 0.73861728 L H-HW-0.423800 0 4.79554562 -4.14684764 1.23026341 L H-HW-0.423800 0 6.04605274 -3.95498834 0.16323939 L O-OW--0.847600 0 3.16882416 3.14969257 4.25063400 L H-HW-0.423800 0 2.95532920 2.57234472 3.43529320 L H-HW-0.423800 0 3.04584297 4.14266981 3.91376106 L O-OW--0.847600 0 3.27948080 -5.16714298 1.69901926 L H-HW-0.423800 0 2.68631024 -4.74505979 0.98631060 L H-HW-0.423800 0 2.69838845 -5.95107243 2.06043996 L O-OW--0.847600 0 -1.23607274 2.60022378 -4.28824141 L H-HW-0.423800 0 -1.36968510 1.68064847 -3.90529225 L H-HW-0.423800 0 -0.21438016 2.78286215 -4.28590581 L O-OW--0.847600 0 1.36801994 3.39197449 -4.39578410 L H-HW-0.423800 0 1.89606292 3.44271062 -3.52170221 L H-HW-0.423800 0 2.01846091 3.30008448 -5.16935051 L O-OW--0.847600 0 1.61355606 -2.40592290 -3.98747917 L H-HW-0.423800 0 0.87336650 -2.63408396 -3.27166558 L H-HW-0.423800 0 2.40492124 -2.90639136 -3.61971395 L O-OW--0.847600 0 5.17914692 2.14279412 1.04921962 L H-HW-0.423800 0 4.51208728 1.55811859 1.69499597 L H-HW-0.423800 0 4.79453093 3.05702789 1.00916819 L O-OW--0.847600 0 -4.79851239 -0.03227942 3.70741132 L H-HW-0.423800 0 -4.73945444 0.27002293 4.68870800 L H-HW-0.423800 0 -3.90573817 -0.46172618 3.47416608 L O-OW--0.847600 0 -0.61933272 -2.71855519 5.89241093 L H-HW-0.423800 0 -0.72454676 -2.98041195 4.95310793 L H-HW-0.423800 0 -1.50983193 -2.27391277 6.06907574 L O-OW--0.847600 0 -2.61813265 2.99849925 2.41190720 L blank line 1 2 1.0 3 2.0 4 2.0 5 2.0 2 6 1.0 3 4 5 6 7 8 1.0 9 1.0 8 9 10 11 1.0 12 1.0 11 12 13 14 1.0 15 1.0 14 15 16 17 1.0 18 1.0 17 18 19 20 1.0 21 1.0 20 21 22 23 1.0 24 1.0 23 24 25 26 1.0 27 1.0 26 27 28 29 1.0 30 1.0 29 30 31 32 1.0 33 1.0 32 33 34 35 1.0 36 1.0 35 36 37 38 1.0 39 1.0 38 39 40 41 1.0 42 1.0 41 42 43 44 1.0 45 1.0 44 45 46 47 1.0 48 1.0 47 48 49 50 1.0 51 1.0 50 51 52 53 1.0 54 1.0 53 54 55 56 1.0 57 1.0 56 57 58 59 1.0 60 1.0 59 60 61 62 1.0 63 1.0 62 63 64 65 1.0 66 1.0 65 66 67 68 1.0 69 1.0 68 69 70 71 1.0 72 1.0 71 72 73 74 1.0 75 1.0 74 75 76 77 1.0 78 1.0 77 78 79 80 1.0 81 1.0 80 81 82 83 1.0 84 1.0 83 84 85 86 1.0 87 1.0 86 87 88 89 1.0 90 1.0 89 90 91 92 1.0 93 1.0 92 93 94 95 1.0 96 1.0 95 96 97 98 1.0 99 1.0 98 99 100 101 1.0 102 1.0 101 102 103 104 1.0 105 1.0 104 105 106 107 1.0 108 1.0 107 108 109 110 1.0 111 1.0 110 111 112 113 1.0 114 1.0 113 114 115 116 1.0 117 1.0 116 117 118 119 1.0 120 1.0 119 120 121 122 1.0 123 1.0 122 123 124 125 1.0 126 1.0 125 126 127 128 1.0 129 1.0 128 129 blank line VDW OW 1.7769 0.1554 VDW S 1.9924 0.2500 VDW O1 1.8380 0.2062 VDW O2 1.8380 0.2062 VDW O3 1.8380 0.2062 VDW O4 1.8380 0.2062 VDW H 0.0000 0.0000 VDW HW 0.0000 0.0000 NonBon 3 1 0 0 0.0 0.0 0.5 0.0 0.0 -1.0 HrmStr1 S O1 556.477 1.634 HrmStr1 S O2 1252.366 1.438 HrmStr1 S O3 1252.366 1.438 HrmStr1 S O4 1252.366 1.438 HrmStr1 O1 H 1090.129 0.949 HrmStr1 OW HW 1108.570 1.000 HrmBnd1 HW OW HW 91.539 109.40 HrmBnd1 O2 S O3 109.22 114.76 HrmBnd1 O2 S O4 109.22 114.76 HrmBnd1 O3 S O4 109.22 114.76 HrmBnd1 O1 S O2 194.67 103.45 HrmBnd1 O1 S O3 194.67 103.45 HrmBnd1 O1 S O4 194.67 103.45 HrmBnd1 H O1 S 95.320 106.39 MM2Tors O2 O3 O4 H 0.000000 0.0000000 0.000000 blank line blank line