From b166b2bf6ac8e7f64bfa28f2800952b1d7b7e65a Mon Sep 17 00:00:00 2001 From: root Date: Sat, 5 Oct 2024 14:42:29 +0800 Subject: [PATCH] remove --- script/S112D/unk.gro | 38 ----- script/S112D/unk.itp | 350 ------------------------------------------ script/S112D/unk.mol2 | 80 ---------- script/S112D/unk.top | 14 -- 4 files changed, 482 deletions(-) delete mode 100755 script/S112D/unk.gro delete mode 100755 script/S112D/unk.itp delete mode 100755 script/S112D/unk.mol2 delete mode 100755 script/S112D/unk.top diff --git a/script/S112D/unk.gro b/script/S112D/unk.gro deleted file mode 100755 index 31330c8..0000000 --- a/script/S112D/unk.gro +++ /dev/null @@ -1,38 +0,0 @@ -unk - 35 - 1MOL O 1 -1.067 0.040 -0.980 - 1MOL O 2 -0.581 -0.528 -0.879 - 1MOL O 3 -0.671 -0.442 -0.698 - 1MOL N 4 -1.239 0.070 -1.216 - 1MOL N 5 -0.947 -0.085 -1.139 - 1MOL N 6 -0.657 -0.446 -0.823 - 1MOL C 7 -0.907 0.272 -1.205 - 1MOL C 8 -1.058 0.240 -1.201 - 1MOL C 9 -1.094 0.091 -1.214 - 1MOL C 10 -0.841 0.221 -1.332 - 1MOL C 11 -0.839 0.210 -1.083 - 1MOL C 12 -1.036 0.013 -1.096 - 1MOL C 13 -0.874 -0.176 -1.059 - 1MOL C 14 -0.789 -0.266 -1.120 - 1MOL C 15 -0.889 -0.172 -0.921 - 1MOL C 16 -0.717 -0.356 -1.041 - 1MOL C 17 -0.817 -0.262 -0.843 - 1MOL C 18 -0.731 -0.354 -0.903 - 1MOL H 19 -0.896 0.381 -1.200 - 1MOL H 20 -1.101 0.281 -1.108 - 1MOL H 21 -1.107 0.295 -1.282 - 1MOL H 22 -1.056 0.053 -1.309 - 1MOL H 23 -0.737 0.256 -1.337 - 1MOL H 24 -0.838 0.112 -1.338 - 1MOL H 25 -0.893 0.259 -1.421 - 1MOL H 26 -0.804 0.108 -1.097 - 1MOL H 27 -0.746 0.267 -1.064 - 1MOL H 28 -0.897 0.220 -0.991 - 1MOL H 29 -1.259 -0.028 -1.234 - 1MOL H 30 -1.280 0.123 -1.293 - 1MOL H 31 -0.931 -0.094 -1.239 - 1MOL H 32 -0.778 -0.269 -1.228 - 1MOL H 33 -0.953 -0.105 -0.867 - 1MOL H 34 -0.651 -0.426 -1.092 - 1MOL H 35 -0.830 -0.258 -0.735 - 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 diff --git a/script/S112D/unk.itp b/script/S112D/unk.itp deleted file mode 100755 index 28aacc3..0000000 --- a/script/S112D/unk.itp +++ /dev/null @@ -1,350 +0,0 @@ -; Created by Sobtop (http://sobereva.com/soft/sobtop) Version 1.0(dev5) on 2024-09-25 - -[ atomtypes ] -; name at.num mass charge ptype sigma (nm) epsilon (kJ/mol) -o 8 15.999405 0.000000 A 2.959922E-01 8.786400E-01 -n3 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01 -n 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01 -no 7 14.006703 0.000000 A 3.249999E-01 7.112800E-01 -c3 6 12.010736 0.000000 A 3.399670E-01 4.577296E-01 -c 6 12.010736 0.000000 A 3.399670E-01 3.598240E-01 -ca 6 12.010736 0.000000 A 3.399670E-01 3.598240E-01 -hc 1 1.007941 0.000000 A 2.649533E-01 6.568880E-02 -h1 1 1.007941 0.000000 A 2.471353E-01 6.568880E-02 -hn 1 1.007941 0.000000 A 1.069078E-01 6.568880E-02 -ha 1 1.007941 0.000000 A 2.599642E-01 6.276000E-02 - -[ moleculetype ] -; name nrexcl -unk 3 - -; Atomic charges are those loaded from .mol2 file -[ atoms ] -; Index type residue resname atom cgnr charge mass - 1 o 1 MOL O 1 0.00000000 15.999405 - 2 o 1 MOL O 2 0.00000000 15.999405 - 3 o 1 MOL O 3 0.00000000 15.999405 - 4 n3 1 MOL N 4 0.00000000 14.006703 - 5 n 1 MOL N 5 0.00000000 14.006703 - 6 no 1 MOL N 6 0.00000000 14.006703 - 7 c3 1 MOL C 7 0.00000000 12.010736 - 8 c3 1 MOL C 8 0.00000000 12.010736 - 9 c3 1 MOL C 9 0.00000000 12.010736 - 10 c3 1 MOL C 10 0.00000000 12.010736 - 11 c3 1 MOL C 11 0.00000000 12.010736 - 12 c 1 MOL C 12 0.00000000 12.010736 - 13 ca 1 MOL C 13 0.00000000 12.010736 - 14 ca 1 MOL C 14 0.00000000 12.010736 - 15 ca 1 MOL C 15 0.00000000 12.010736 - 16 ca 1 MOL C 16 0.00000000 12.010736 - 17 ca 1 MOL C 17 0.00000000 12.010736 - 18 ca 1 MOL C 18 0.00000000 12.010736 - 19 hc 1 MOL H 19 0.00000000 1.007941 - 20 hc 1 MOL H 20 0.00000000 1.007941 - 21 hc 1 MOL H 21 0.00000000 1.007941 - 22 h1 1 MOL H 22 0.00000000 1.007941 - 23 hc 1 MOL H 23 0.00000000 1.007941 - 24 hc 1 MOL H 24 0.00000000 1.007941 - 25 hc 1 MOL H 25 0.00000000 1.007941 - 26 hc 1 MOL H 26 0.00000000 1.007941 - 27 hc 1 MOL H 27 0.00000000 1.007941 - 28 hc 1 MOL H 28 0.00000000 1.007941 - 29 hn 1 MOL H 29 0.00000000 1.007941 - 30 hn 1 MOL H 30 0.00000000 1.007941 - 31 hn 1 MOL H 31 0.00000000 1.007941 - 32 ha 1 MOL H 32 0.00000000 1.007941 - 33 ha 1 MOL H 33 0.00000000 1.007941 - 34 ha 1 MOL H 34 0.00000000 1.007941 - 35 ha 1 MOL H 35 0.00000000 1.007941 - -[ bonds ] -; atom_i atom_j functype r0 (nm) k (kJ/mol/nm^2) - 1 12 1 0.121830 5.336274E+05 ; O-C, prebuilt c-o - 2 6 1 0.122600 6.207382E+05 ; O-N, prebuilt no-o - 3 6 1 0.122600 6.207382E+05 ; O-N, prebuilt no-o - 4 9 1 0.146470 2.727131E+05 ; N-C, prebuilt c3-n3 - 4 29 1 0.101900 3.283603E+05 ; N-H, prebuilt hn-n3 - 4 30 1 0.101900 3.283603E+05 ; N-H, prebuilt hn-n3 - 5 12 1 0.137890 3.578157E+05 ; N-C, prebuilt c-n - 5 13 1 0.141210 3.214986E+05 ; N-C, prebuilt ca-n - 5 31 1 0.101290 3.373978E+05 ; N-H, prebuilt hn-n - 6 18 1 0.146890 2.691986E+05 ; N-C, prebuilt ca-no - 7 8 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 7 10 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 7 11 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 7 19 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 8 9 1 0.153750 2.517931E+05 ; C-C, prebuilt c3-c3 - 8 20 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 8 21 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 9 12 1 0.152410 2.619184E+05 ; C-C, prebuilt c-c3 - 9 22 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-h1 - 10 23 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 10 24 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 10 25 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 11 26 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 11 27 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 11 28 1 0.109690 2.766461E+05 ; C-H, prebuilt c3-hc - 13 14 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 13 15 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 14 16 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 14 32 1 0.108600 2.893654E+05 ; C-H, prebuilt ca-ha - 15 17 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 15 33 1 0.108600 2.893654E+05 ; C-H, prebuilt ca-ha - 16 18 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 16 34 1 0.108600 2.893654E+05 ; C-H, prebuilt ca-ha - 17 18 1 0.139840 3.858485E+05 ; C-C, prebuilt ca-ca - 17 35 1 0.108600 2.893654E+05 ; C-H, prebuilt ca-ha - -[ angles ] -; atom_i atom_j atom_k functype a0 (Deg.) k (kJ/mol/rad^2) - 9 4 29 1 109.290 3.966432E+02 ; C-N-H, prebuilt c3-n3-hn - 9 4 30 1 109.290 3.966432E+02 ; C-N-H, prebuilt c3-n3-hn - 29 4 30 1 106.400 3.464352E+02 ; H-N-H, prebuilt hn-n3-hn - 12 5 13 1 123.710 5.338784E+02 ; C-N-C, prebuilt c-n-ca - 12 5 31 1 117.550 4.041744E+02 ; C-N-H, prebuilt c-n-hn - 13 5 31 1 116.000 3.983168E+02 ; C-N-H, prebuilt ca-n-hn - 2 6 3 1 125.080 6.418256E+02 ; O-N-O, prebuilt o-no-o - 2 6 18 1 117.760 5.748816E+02 ; O-N-C, prebuilt ca-no-o - 3 6 18 1 117.760 5.748816E+02 ; O-N-C, prebuilt ca-no-o - 8 7 10 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 8 7 11 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 8 7 19 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 10 7 11 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 10 7 19 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 11 7 19 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 7 8 9 1 111.510 5.263472E+02 ; C-C-C, prebuilt c3-c3-c3 - 7 8 20 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 7 8 21 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 9 8 20 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 9 8 21 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 20 8 21 1 107.580 3.296992E+02 ; H-C-H, prebuilt hc-c3-hc - 4 9 8 1 111.040 5.522880E+02 ; N-C-C, prebuilt c3-c3-n3 - 4 9 12 1 111.140 5.547984E+02 ; N-C-C, prebuilt c-c3-n3 - 4 9 22 1 109.880 4.142160E+02 ; N-C-H, prebuilt h1-c3-n3 - 8 9 12 1 111.040 5.296944E+02 ; C-C-C, prebuilt c-c3-c3 - 8 9 22 1 109.560 3.882752E+02 ; C-C-H, prebuilt c3-c3-h1 - 12 9 22 1 108.220 3.932960E+02 ; C-C-H, prebuilt c-c3-h1 - 7 10 23 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 7 10 24 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 7 10 25 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 23 10 24 1 107.580 3.296992E+02 ; H-C-H, prebuilt hc-c3-hc - 23 10 25 1 107.580 3.296992E+02 ; H-C-H, prebuilt hc-c3-hc - 24 10 25 1 107.580 3.296992E+02 ; H-C-H, prebuilt hc-c3-hc - 7 11 26 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 7 11 27 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 7 11 28 1 109.800 3.874384E+02 ; C-C-H, prebuilt c3-c3-hc - 26 11 27 1 107.580 3.296992E+02 ; H-C-H, prebuilt hc-c3-hc - 26 11 28 1 107.580 3.296992E+02 ; H-C-H, prebuilt hc-c3-hc - 27 11 28 1 107.580 3.296992E+02 ; H-C-H, prebuilt hc-c3-hc - 1 12 5 1 123.050 6.209056E+02 ; O-C-N, prebuilt n-c-o - 1 12 9 1 123.200 5.640032E+02 ; O-C-C, prebuilt c3-c-o - 5 12 9 1 115.180 5.589824E+02 ; N-C-C, prebuilt c3-c-n - 5 13 14 1 120.190 5.681872E+02 ; N-C-C, prebuilt ca-ca-n - 5 13 15 1 120.190 5.681872E+02 ; N-C-C, prebuilt ca-ca-n - 14 13 15 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 13 14 16 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 13 14 32 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 16 14 32 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 13 15 17 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 13 15 33 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 17 15 33 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 14 16 18 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 14 16 34 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 18 16 34 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 15 17 18 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - 15 17 35 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 18 17 35 1 119.880 4.033376E+02 ; C-C-H, prebuilt ca-ca-ha - 6 18 16 1 119.010 5.589824E+02 ; N-C-C, prebuilt ca-ca-no - 6 18 17 1 119.010 5.589824E+02 ; N-C-C, prebuilt ca-ca-no - 16 18 17 1 120.020 5.573088E+02 ; C-C-C, prebuilt ca-ca-ca - -[ dihedrals ] ; propers -; atom_i atom_j atom_k atom_l functype d0 (Deg.) k (kJ/mol/rad^2) ; Case of functype=2 -; atom_i atom_j atom_k atom_l functype phase (Deg.) kd (kJ/mol) pn ; Case of functype=9 - 1 12 5 13 9 180.000 10.46000 2 ; O-C-N-C, prebuilt X-c-n-X - 1 12 5 31 9 180.000 10.46000 2 ; O-C-N-H, prebuilt hn-n-c-o - 1 12 5 31 9 0.000 8.36800 1 ; O-C-N-H, prebuilt hn-n-c-o - 1 12 9 4 9 180.000 0.00000 2 ; O-C-C-N, prebuilt X-c-c3-X - 1 12 9 8 9 180.000 0.00000 2 ; O-C-C-C, prebuilt X-c-c3-X - 1 12 9 22 9 0.000 3.34720 1 ; O-C-C-H, prebuilt h1-c3-c-o - 1 12 9 22 9 0.000 0.00000 2 ; O-C-C-H, prebuilt h1-c3-c-o - 1 12 9 22 9 180.000 0.33472 3 ; O-C-C-H, prebuilt h1-c3-c-o - 2 6 18 16 9 180.000 2.51040 2 ; O-N-C-C, prebuilt X-ca-no-X - 2 6 18 17 9 180.000 2.51040 2 ; O-N-C-C, prebuilt X-ca-no-X - 3 6 18 16 9 180.000 2.51040 2 ; O-N-C-C, prebuilt X-ca-no-X - 3 6 18 17 9 180.000 2.51040 2 ; O-N-C-C, prebuilt X-ca-no-X - 4 9 8 7 9 0.000 0.65084 3 ; N-C-C-C, prebuilt X-c3-c3-X - 4 9 8 20 9 0.000 0.65084 3 ; N-C-C-H, prebuilt X-c3-c3-X - 4 9 8 21 9 0.000 0.65084 3 ; N-C-C-H, prebuilt X-c3-c3-X - 4 9 12 5 9 180.000 0.00000 2 ; N-C-C-N, prebuilt X-c-c3-X - 5 12 9 8 9 0.000 0.41840 4 ; N-C-C-C, prebuilt c3-c3-c-n - 5 12 9 8 9 0.000 0.29288 2 ; N-C-C-C, prebuilt c3-c3-c-n - 5 12 9 22 9 180.000 0.00000 2 ; N-C-C-H, prebuilt X-c-c3-X - 5 13 14 16 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 5 13 14 32 9 180.000 15.16700 2 ; N-C-C-H, prebuilt X-ca-ca-X - 5 13 15 17 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 5 13 15 33 9 180.000 15.16700 2 ; N-C-C-H, prebuilt X-ca-ca-X - 6 18 16 14 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 6 18 16 34 9 180.000 15.16700 2 ; N-C-C-H, prebuilt X-ca-ca-X - 6 18 17 15 9 180.000 15.16700 2 ; N-C-C-C, prebuilt X-ca-ca-X - 6 18 17 35 9 180.000 15.16700 2 ; N-C-C-H, prebuilt X-ca-ca-X - 7 8 9 12 9 0.000 0.65084 3 ; C-C-C-C, prebuilt X-c3-c3-X - 7 8 9 22 9 0.000 0.65084 3 ; C-C-C-H, prebuilt X-c3-c3-X - 8 7 10 23 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 8 7 10 24 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 8 7 10 25 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 8 7 11 26 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 8 7 11 27 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 8 7 11 28 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 8 9 4 29 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 8 9 4 30 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 9 8 7 10 9 0.000 0.75312 3 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 9 8 7 10 9 180.000 1.04600 2 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 9 8 7 10 9 180.000 0.83680 1 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 9 8 7 11 9 0.000 0.75312 3 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 9 8 7 11 9 180.000 1.04600 2 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 9 8 7 11 9 180.000 0.83680 1 ; C-C-C-C, prebuilt c3-c3-c3-c3 - 9 8 7 19 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 9 12 5 13 9 180.000 10.46000 2 ; C-C-N-C, prebuilt X-c-n-X - 9 12 5 31 9 180.000 10.46000 2 ; C-C-N-H, prebuilt X-c-n-X - 10 7 8 20 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 10 7 8 21 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 10 7 11 26 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 10 7 11 27 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 10 7 11 28 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 11 7 8 20 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 11 7 8 21 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 11 7 10 23 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 11 7 10 24 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 11 7 10 25 9 0.000 0.66944 3 ; C-C-C-H, prebuilt hc-c3-c3-c3 - 12 5 13 14 9 180.000 1.88280 2 ; C-N-C-C, prebuilt X-ca-n-X - 12 5 13 15 9 180.000 1.88280 2 ; C-N-C-C, prebuilt X-ca-n-X - 12 9 4 29 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 12 9 4 30 9 0.000 1.25520 3 ; C-C-N-H, prebuilt X-c3-n3-X - 12 9 8 20 9 0.000 0.65084 3 ; C-C-C-H, prebuilt X-c3-c3-X - 12 9 8 21 9 0.000 0.65084 3 ; C-C-C-H, prebuilt X-c3-c3-X - 13 14 16 18 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 13 14 16 34 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 13 15 17 18 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 13 15 17 35 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 14 13 5 31 9 180.000 1.88280 2 ; C-C-N-H, prebuilt X-ca-n-X - 14 13 15 17 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 14 13 15 33 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 14 16 18 17 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 15 13 5 31 9 180.000 1.88280 2 ; C-C-N-H, prebuilt X-ca-n-X - 15 13 14 16 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 15 13 14 32 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 15 17 18 16 9 180.000 15.16700 2 ; C-C-C-C, prebuilt X-ca-ca-X - 16 18 17 35 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 17 18 16 34 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 18 16 14 32 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 18 17 15 33 9 180.000 15.16700 2 ; C-C-C-H, prebuilt X-ca-ca-X - 19 7 8 20 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 19 7 8 21 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 19 7 10 23 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 19 7 10 24 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 19 7 10 25 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 19 7 11 26 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 19 7 11 27 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 19 7 11 28 9 0.000 0.62760 3 ; H-C-C-H, prebuilt hc-c3-c3-hc - 20 8 9 22 9 0.000 0.65084 3 ; H-C-C-H, prebuilt X-c3-c3-X - 21 8 9 22 9 0.000 0.65084 3 ; H-C-C-H, prebuilt X-c3-c3-X - 22 9 4 29 9 0.000 1.25520 3 ; H-C-N-H, prebuilt X-c3-n3-X - 22 9 4 30 9 0.000 1.25520 3 ; H-C-N-H, prebuilt X-c3-n3-X - 32 14 16 34 9 180.000 15.16700 2 ; H-C-C-H, prebuilt X-ca-ca-X - 33 15 17 35 9 180.000 15.16700 2 ; H-C-C-H, prebuilt X-ca-ca-X - -[ pairs ] ; Yielded based on rotatable dihedrals -; atom_i atom_j functype - 1 13 1 ; O-C-N-C - 1 31 1 ; O-C-N-H - 1 4 1 ; O-C-C-N - 1 8 1 ; O-C-C-C - 1 22 1 ; O-C-C-H - 2 16 1 ; O-N-C-C - 2 17 1 ; O-N-C-C - 3 16 1 ; O-N-C-C - 3 17 1 ; O-N-C-C - 4 7 1 ; N-C-C-C - 4 20 1 ; N-C-C-H - 4 21 1 ; N-C-C-H - 4 5 1 ; N-C-C-N - 5 8 1 ; N-C-C-C - 5 22 1 ; N-C-C-H - 5 16 1 ; N-C-C-C - 5 32 1 ; N-C-C-H - 5 17 1 ; N-C-C-C - 5 33 1 ; N-C-C-H - 6 14 1 ; N-C-C-C - 6 34 1 ; N-C-C-H - 6 15 1 ; N-C-C-C - 6 35 1 ; N-C-C-H - 7 12 1 ; C-C-C-C - 7 22 1 ; C-C-C-H - 8 23 1 ; C-C-C-H - 8 24 1 ; C-C-C-H - 8 25 1 ; C-C-C-H - 8 26 1 ; C-C-C-H - 8 27 1 ; C-C-C-H - 8 28 1 ; C-C-C-H - 8 29 1 ; C-C-N-H - 8 30 1 ; C-C-N-H - 9 10 1 ; C-C-C-C - 9 11 1 ; C-C-C-C - 9 19 1 ; C-C-C-H - 9 13 1 ; C-C-N-C - 9 31 1 ; C-C-N-H - 10 20 1 ; C-C-C-H - 10 21 1 ; C-C-C-H - 10 26 1 ; C-C-C-H - 10 27 1 ; C-C-C-H - 10 28 1 ; C-C-C-H - 11 20 1 ; C-C-C-H - 11 21 1 ; C-C-C-H - 11 23 1 ; C-C-C-H - 11 24 1 ; C-C-C-H - 11 25 1 ; C-C-C-H - 12 14 1 ; C-N-C-C - 12 15 1 ; C-N-C-C - 12 29 1 ; C-C-N-H - 12 30 1 ; C-C-N-H - 12 20 1 ; C-C-C-H - 12 21 1 ; C-C-C-H - 13 18 1 ; C-C-C-C - 13 34 1 ; C-C-C-H - 13 35 1 ; C-C-C-H - 14 31 1 ; C-C-N-H - 14 17 1 ; C-C-C-C - 14 33 1 ; C-C-C-H - 15 31 1 ; C-C-N-H - 15 16 1 ; C-C-C-C - 15 32 1 ; C-C-C-H - 16 35 1 ; C-C-C-H - 17 34 1 ; C-C-C-H - 18 32 1 ; C-C-C-H - 18 33 1 ; C-C-C-H - 19 20 1 ; H-C-C-H - 19 21 1 ; H-C-C-H - 19 23 1 ; H-C-C-H - 19 24 1 ; H-C-C-H - 19 25 1 ; H-C-C-H - 19 26 1 ; H-C-C-H - 19 27 1 ; H-C-C-H - 19 28 1 ; H-C-C-H - 20 22 1 ; H-C-C-H - 21 22 1 ; H-C-C-H - 22 29 1 ; H-C-N-H - 22 30 1 ; H-C-N-H - 32 34 1 ; H-C-C-H - 33 35 1 ; H-C-C-H - -[ dihedrals ] ; impropers -; atom_i atom_j atom_k atom_l functype phase (Deg.) kd (kJ/mol) pn - 12 13 5 31 4 180.000 4.60240 2 ; C-C-N-H, prebuilt X-X-n-hn - 1 5 12 9 4 180.000 43.93200 2 ; O-N-C-C, prebuilt X-X-c-o - 5 14 13 15 4 180.000 4.60240 2 ; N-C-C-C, guess (same as GAFF X -X -ca-ha) - 13 16 14 32 4 180.000 4.60240 2 ; C-C-C-H, prebuilt X-X-ca-ha - 13 17 15 33 4 180.000 4.60240 2 ; C-C-C-H, prebuilt X-X-ca-ha - 14 18 16 34 4 180.000 4.60240 2 ; C-C-C-H, prebuilt X-X-ca-ha - 15 18 17 35 4 180.000 4.60240 2 ; C-C-C-H, prebuilt X-X-ca-ha - 6 16 18 17 4 180.000 4.60240 2 ; N-C-C-C, guess (same as GAFF X -X -ca-ha) diff --git a/script/S112D/unk.mol2 b/script/S112D/unk.mol2 deleted file mode 100755 index 4c4ff5e..0000000 --- a/script/S112D/unk.mol2 +++ /dev/null @@ -1,80 +0,0 @@ -# created with PyMOL 3.0.0 -@MOLECULE -UNK -35 35 1 -SMALL -USER_CHARGES -@ATOM -1 O -10.669 0.397 -9.796 O.2 1 UNK 0.000 -2 O -5.807 -5.276 -8.787 O.2 1 UNK 0.000 -3 O -6.714 -4.423 -6.979 O.2 1 UNK 0.000 -4 N -12.391 0.704 -12.159 N.3 1 UNK 0.000 -5 N -9.471 -0.846 -11.385 N.pl3 1 UNK 0.000 -6 N -6.575 -4.458 -8.226 N.pl3 1 UNK 0.000 -7 C -9.074 2.716 -12.046 C.3 1 UNK 0.000 -8 C -10.583 2.398 -12.007 C.3 1 UNK 0.000 -9 C -10.943 0.909 -12.141 C.3 1 UNK 0.000 -10 C -8.406 2.209 -13.324 C.3 1 UNK 0.000 -11 C -8.385 2.100 -10.825 C.3 1 UNK 0.000 -12 C -10.364 0.133 -10.956 C.2 1 UNK 0.000 -13 C -8.739 -1.758 -10.588 C.2 1 UNK 0.000 -14 C -7.890 -2.664 -11.201 C.2 1 UNK 0.000 -15 C -8.889 -1.725 -9.211 C.2 1 UNK 0.000 -16 C -7.170 -3.563 -10.414 C.2 1 UNK 0.000 -17 C -8.168 -2.624 -8.425 C.2 1 UNK 0.000 -18 C -7.309 -3.543 -9.026 C.2 1 UNK 0.000 -19 H -8.963 3.807 -11.998 H 1 UNK 0.000 -20 H -11.006 2.805 -11.078 H 1 UNK 0.000 -21 H -11.065 2.951 -12.825 H 1 UNK 0.000 -22 H -10.556 0.526 -13.090 H 1 UNK 0.000 -23 H -7.369 2.559 -13.373 H 1 UNK 0.000 -24 H -8.383 1.117 -13.384 H 1 UNK 0.000 -25 H -8.926 2.589 -14.210 H 1 UNK 0.000 -26 H -8.036 1.080 -10.971 H 1 UNK 0.000 -27 H -7.463 2.669 -10.641 H 1 UNK 0.000 -28 H -8.970 2.203 -9.907 H 1 UNK 0.000 -29 H -12.594 -0.278 -12.341 H 1 UNK 0.000 -30 H -12.801 1.228 -12.931 H 1 UNK 0.000 -31 H -9.311 -0.937 -12.386 H 1 UNK 0.000 -32 H -7.775 -2.687 -12.281 H 1 UNK 0.000 -33 H -9.533 -1.047 -8.672 H 1 UNK 0.000 -34 H -6.509 -4.265 -10.917 H 1 UNK 0.000 -35 H -8.301 -2.580 -7.347 H 1 UNK 0.000 -@BOND -1 1 12 2 -2 2 6 1 -3 3 6 2 -4 4 9 1 -5 4 29 1 -6 4 30 1 -7 5 12 1 -8 5 13 1 -9 5 31 1 -10 6 18 1 -11 7 8 1 -12 7 10 1 -13 7 11 1 -14 7 19 1 -15 8 9 1 -16 8 20 1 -17 8 21 1 -18 9 12 1 -19 9 22 1 -20 10 23 1 -21 10 24 1 -22 10 25 1 -23 11 26 1 -24 11 27 1 -25 11 28 1 -26 13 14 2 -27 13 15 1 -28 14 16 1 -29 14 32 1 -30 15 17 2 -31 15 33 1 -32 16 18 2 -33 16 34 1 -34 17 18 1 -35 17 35 1 -@SUBSTRUCTURE -1 UNK0 1 GROUP 1 **** UNK diff --git a/script/S112D/unk.top b/script/S112D/unk.top deleted file mode 100755 index 533ff23..0000000 --- a/script/S112D/unk.top +++ /dev/null @@ -1,14 +0,0 @@ -; Created by Sobtop (http://sobereva.com/soft/sobtop) Version 1.0(dev5) on 2024-09-25 - -[ defaults ] -; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ - 1 2 yes 0.5 0.8333 - -#include "unk.itp" - -[ system ] -unk - -[ molecules ] -; Molecule nmols -unk 1