# HG changeset patch
# User chemteam
# Date 1560420994 14400
# Node ID 2e202f6c3034042f6591f65e4a36a134aa838a37
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1620d2eb7fd3ea43bb4dfe6cee5b45015fd13a3
diff -r 000000000000 -r 2e202f6c3034 acpype.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/acpype.xml Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,73 @@
+
+ using acpype
+
+ macros.xml
+
+
+ acpype
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ save_gro
+
+
+
+
+
+
+
+
+
+
+
+
+ doi:10.1186/1756-0500-5-367
+
+
diff -r 000000000000 -r 2e202f6c3034 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,20 @@
+
+ 19.0
+
+
+ ambertools
+
+
+
+
+
+ 10.1002/jcc.20290
+
+ @misc{ambertools, author = {D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, S. Izadi, A.
+ Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo,
+ J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman }, year = {2018}, title = {AMBER 2018}, publisher = {University of California, San Francisco}, url =
+ {http://ambermd.org/CiteAmber.php}, }
+
+
+
+
diff -r 000000000000 -r 2e202f6c3034 test-data/JZ4.mol2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/JZ4.mol2 Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,52 @@
+@MOLECULE
+/data/dnb02/galaxy_db/files/009/501/dataset_9501918.dat
+ 22 22 0 0 0
+SMALL
+GASTEIGER
+
+@ATOM
+ 1 C4 0.7939 1.3702 2.1983 C.3 167 JZ4167 -0.0650
+ 2 C7 6.5984 0.4172 2.4451 C.ar 167 JZ4167 -0.0613
+ 3 C8 7.3182 0.9119 1.3612 C.ar 167 JZ4167 -0.0583
+ 4 C9 6.6461 1.3322 0.2147 C.ar 167 JZ4167 -0.0199
+ 5 C10 5.2522 1.2617 0.1608 C.ar 167 JZ4167 0.1200
+ 6 C11 5.2053 0.3427 2.3837 C.ar 167 JZ4167 -0.0551
+ 7 C12 4.5084 0.7745 1.2426 C.ar 167 JZ4167 -0.0060
+ 8 C13 3.0004 0.6682 1.1973 C.3 167 JZ4167 -0.0245
+ 9 C14 2.3079 1.4796 2.2975 C.3 167 JZ4167 -0.0518
+ 10 OAB 4.5987 1.6713 -0.9677 O.3 167 JZ4167 -0.5065
+ 11 H 0.3197 1.9287 3.0114 H 167 JZ4167 0.0230
+ 12 H 0.4705 0.3267 2.2700 H 167 JZ4167 0.0230
+ 13 H 0.4322 1.7786 1.2494 H 167 JZ4167 0.0230
+ 14 H 7.1195 0.0849 3.3395 H 167 JZ4167 0.0618
+ 15 H 8.4028 0.9664 1.4088 H 167 JZ4167 0.0619
+ 16 H 7.2222 1.7087 -0.6246 H 167 JZ4167 0.0654
+ 17 H 4.6638 -0.0590 3.2368 H 167 JZ4167 0.0621
+ 18 H 2.7296 -0.3918 1.2845 H 167 JZ4167 0.0314
+ 19 H 2.6172 0.9976 0.2247 H 167 JZ4167 0.0314
+ 20 H 2.6004 2.5342 2.2276 H 167 JZ4167 0.0266
+ 21 H 2.6177 1.1288 3.2886 H 167 JZ4167 0.0266
+ 22 H 5.2561 1.9626 -1.6199 H 167 JZ4167 0.2921
+@BOND
+ 1 4 3 ar
+ 2 4 5 ar
+ 3 3 2 ar
+ 4 10 5 1
+ 5 5 7 ar
+ 6 2 6 ar
+ 7 7 6 ar
+ 8 7 8 1
+ 9 8 9 1
+ 10 9 1 1
+ 11 1 11 1
+ 12 1 12 1
+ 13 1 13 1
+ 14 2 14 1
+ 15 3 15 1
+ 16 4 16 1
+ 17 6 17 1
+ 18 8 18 1
+ 19 8 19 1
+ 20 9 20 1
+ 21 9 21 1
+ 22 10 22 1
diff -r 000000000000 -r 2e202f6c3034 test-data/LigA.mol2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA.mol2 Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,61 @@
+@MOLECULE
+LigA
+24 24 1 0 0
+SMALL
+USER_CHARGES
+
+
+@ATOM
+ 1 C 49.2110 26.9920 85.5530 C.2 1 <1> -0.3000
+ 2 H 49.1050 28.0330 85.7020 H 1 <1> 0.1500
+ 3 H 48.8320 26.6060 84.6410 H 1 <1> 0.1500
+ 4 C 49.8460 26.1960 86.4430 C.2 1 <1> -0.1733
+ 5 C 50.0590 24.7460 86.2630 C.2 1 <1> 1.0500
+ 6 O 50.4810 24.0440 87.2160 O.co2 1 <1> -0.9000
+ 7 O 49.8330 24.2110 85.1490 O.co2 1 <1> -0.9000
+ 8 O 50.3730 26.8140 87.5890 O.3 1 <1> -0.3567
+ 9 C 51.7280 27.3660 87.5930 C.3 1 <1> 0.3382
+ 10 H 51.8840 27.9250 88.5040 H 1 <1> 0.0800
+ 11 C 51.8170 28.2920 86.3980 C.2 1 <1> -0.2882
+ 12 H 51.3990 29.2560 86.5300 H 1 <1> 0.1500
+ 13 C 52.1840 27.8630 85.1670 C.2 1 <1> -0.2500
+ 14 C 52.8190 26.5610 85.0450 C.2 1 <1> -0.1500
+ 15 H 53.0370 26.2220 84.0630 H 1 <1> 0.1500
+ 16 C 53.1170 25.8090 86.1190 C.2 1 <1> -0.2882
+ 17 H 53.5700 24.8590 86.0130 H 1 <1> 0.1500
+ 18 C 52.7610 26.1980 87.5410 C.3 1 <1> 0.3382
+ 19 H 52.3530 25.3480 88.0710 H 1 <1> 0.0800
+ 20 O 54.0020 26.6280 88.1730 O.3 1 <1> -0.6800
+ 21 H 54.4570 27.1880 87.5220 H 1 <1> 0.4000
+ 22 C 51.9410 28.6780 83.9640 C.2 1 <1> 1.0500
+ 23 O 51.9100 29.9280 84.0860 O.co2 1 <1> -0.9000
+ 24 O 51.8570 28.1570 82.8230 O.co2 1 <1> -0.9000
+@BOND
+ 1 1 2 1
+ 2 1 3 1
+ 3 1 4 2
+ 4 4 5 1
+ 5 4 8 1
+ 6 5 6 ar
+ 7 5 7 ar
+ 8 8 9 1
+ 9 9 10 1
+ 10 9 11 1
+ 11 9 18 1
+ 12 11 12 1
+ 13 11 13 2
+ 14 13 14 1
+ 15 13 22 1
+ 16 14 15 1
+ 17 14 16 2
+ 18 16 17 1
+ 19 16 18 1
+ 20 18 19 1
+ 21 18 20 1
+ 22 20 21 1
+ 23 22 23 ar
+ 24 22 24 ar
+@SUBSTRUCTURE
+ 1 **** 13 GROUP 4 **** **** 0
+
+# MOE 2016.08 (io_trps.svl 2016.04)
diff -r 000000000000 -r 2e202f6c3034 test-data/LigA.pdb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA.pdb Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,26 @@
+CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
+ATOM 1 C <1> X 1 49.211 26.992 85.553 0.00 0.00
+ATOM 2 H <1> X 1 49.105 28.033 85.702 0.00 0.00
+ATOM 3 H <1> X 1 48.832 26.606 84.641 0.00 0.00
+ATOM 4 C <1> X 1 49.846 26.196 86.443 0.00 0.00
+ATOM 5 C <1> X 1 50.059 24.746 86.263 0.00 0.00
+ATOM 6 O <1> X 1 50.481 24.044 87.216 0.00 0.00
+ATOM 7 O <1> X 1 49.833 24.211 85.149 0.00 0.00
+ATOM 8 O <1> X 1 50.373 26.814 87.589 0.00 0.00
+ATOM 9 C <1> X 1 51.728 27.366 87.593 0.00 0.00
+ATOM 10 H <1> X 1 51.884 27.925 88.504 0.00 0.00
+ATOM 11 C <1> X 1 51.817 28.292 86.398 0.00 0.00
+ATOM 12 H <1> X 1 51.399 29.256 86.530 0.00 0.00
+ATOM 13 C <1> X 1 52.184 27.863 85.167 0.00 0.00
+ATOM 14 C <1> X 1 52.819 26.561 85.045 0.00 0.00
+ATOM 15 H <1> X 1 53.037 26.222 84.063 0.00 0.00
+ATOM 16 C <1> X 1 53.117 25.809 86.119 0.00 0.00
+ATOM 17 H <1> X 1 53.570 24.859 86.013 0.00 0.00
+ATOM 18 C <1> X 1 52.761 26.198 87.541 0.00 0.00
+ATOM 19 H <1> X 1 52.353 25.348 88.071 0.00 0.00
+ATOM 20 O <1> X 1 54.002 26.628 88.173 0.00 0.00
+ATOM 21 H <1> X 1 54.457 27.188 87.522 0.00 0.00
+ATOM 22 C <1> X 1 51.941 28.678 83.964 0.00 0.00
+ATOM 23 O <1> X 1 51.910 29.928 84.086 0.00 0.00
+ATOM 24 O <1> X 1 51.857 28.157 82.823 0.00 0.00
+END
diff -r 000000000000 -r 2e202f6c3034 test-data/LigA_output.mol2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.mol2 Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,59 @@
+@MOLECULE
+MOL
+ 24 24 1 0 0
+SMALL
+bcc
+
+
+@ATOM
+ 1 C 49.2110 26.9920 85.5530 c2 1 MOL -0.311000
+ 2 H 49.1050 28.0330 85.7020 ha 1 MOL 0.109500
+ 3 H1 48.8320 26.6060 84.6410 ha 1 MOL 0.109500
+ 4 C1 49.8460 26.1960 86.4430 ce 1 MOL 0.022900
+ 5 C2 50.0590 24.7460 86.2630 ce 1 MOL 0.384200
+ 6 O 50.4810 24.0440 87.2160 o 1 MOL -0.575500
+ 7 O1 49.8330 24.2110 85.1490 o 1 MOL -0.575500
+ 8 O2 50.3730 26.8140 87.5890 os 1 MOL -0.351900
+ 9 C3 51.7280 27.3660 87.5930 c3 1 MOL 0.157300
+ 10 H2 51.8840 27.9250 88.5040 h1 1 MOL 0.051700
+ 11 C4 51.8170 28.2920 86.3980 c2 1 MOL -0.174200
+ 12 H3 51.3990 29.2560 86.5300 ha 1 MOL 0.141000
+ 13 C5 52.1840 27.8630 85.1670 ce 1 MOL -0.149200
+ 14 C6 52.8190 26.5610 85.0450 ce 1 MOL -0.081000
+ 15 H4 53.0370 26.2220 84.0630 ha 1 MOL 0.142000
+ 16 C7 53.1170 25.8090 86.1190 c2 1 MOL -0.248200
+ 17 H5 53.5700 24.8590 86.0130 ha 1 MOL 0.104000
+ 18 C8 52.7610 26.1980 87.5410 c3 1 MOL 0.131300
+ 19 H6 52.3530 25.3480 88.0710 h1 1 MOL 0.151700
+ 20 O3 54.0020 26.6280 88.1730 oh 1 MOL -0.611800
+ 21 H7 54.4570 27.1880 87.5220 ho 1 MOL 0.374000
+ 22 C9 51.9410 28.6780 83.9640 ce 1 MOL 0.376200
+ 23 O4 51.9100 29.9280 84.0860 o 1 MOL -0.587000
+ 24 O5 51.8570 28.1570 82.8230 o 1 MOL -0.587000
+@BOND
+ 1 1 2 1
+ 2 1 3 1
+ 3 1 4 2
+ 4 4 5 1
+ 5 4 8 1
+ 6 5 6 2
+ 7 5 7 1
+ 8 8 9 1
+ 9 9 10 1
+ 10 9 11 1
+ 11 9 18 1
+ 12 11 12 1
+ 13 11 13 2
+ 14 13 14 1
+ 15 13 22 1
+ 16 14 15 1
+ 17 14 16 2
+ 18 16 17 1
+ 19 16 18 1
+ 20 18 19 1
+ 21 18 20 1
+ 22 20 21 1
+ 23 22 23 2
+ 24 22 24 1
+@SUBSTRUCTURE
+ 1 MOL 1 TEMP 0 **** **** 0 ROOT
diff -r 000000000000 -r 2e202f6c3034 test-data/LigA_output.pdb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.pdb Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,24 @@
+ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C
+ATOM 2 H MOL 1 49.105 28.033 85.702 1.00 0.00 H
+ATOM 3 H1 MOL 1 48.832 26.606 84.641 1.00 0.00 H
+ATOM 4 C1 MOL 1 49.846 26.196 86.443 1.00 0.00 C
+ATOM 5 C2 MOL 1 50.059 24.746 86.263 1.00 0.00 C
+ATOM 6 O MOL 1 50.481 24.044 87.216 1.00 0.00 O
+ATOM 7 O1 MOL 1 49.833 24.211 85.149 1.00 0.00 O
+ATOM 8 O2 MOL 1 50.373 26.814 87.589 1.00 0.00 O
+ATOM 9 C3 MOL 1 51.728 27.366 87.593 1.00 0.00 C
+ATOM 10 H2 MOL 1 51.884 27.925 88.504 1.00 0.00 H
+ATOM 11 C4 MOL 1 51.817 28.292 86.398 1.00 0.00 C
+ATOM 12 H3 MOL 1 51.399 29.256 86.530 1.00 0.00 H
+ATOM 13 C5 MOL 1 52.184 27.863 85.167 1.00 0.00 C
+ATOM 14 C6 MOL 1 52.819 26.561 85.045 1.00 0.00 C
+ATOM 15 H4 MOL 1 53.037 26.222 84.063 1.00 0.00 H
+ATOM 16 C7 MOL 1 53.117 25.809 86.119 1.00 0.00 C
+ATOM 17 H5 MOL 1 53.570 24.859 86.013 1.00 0.00 H
+ATOM 18 C8 MOL 1 52.761 26.198 87.541 1.00 0.00 C
+ATOM 19 H6 MOL 1 52.353 25.348 88.071 1.00 0.00 H
+ATOM 20 O3 MOL 1 54.002 26.628 88.173 1.00 0.00 O
+ATOM 21 H7 MOL 1 54.457 27.188 87.522 1.00 0.00 H
+ATOM 22 C9 MOL 1 51.941 28.678 83.964 1.00 0.00 C
+ATOM 23 O4 MOL 1 51.910 29.928 84.086 1.00 0.00 O
+ATOM 24 O5 MOL 1 51.857 28.157 82.823 1.00 0.00 O
diff -r 000000000000 -r 2e202f6c3034 test-data/LigA_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_output.txt Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,21 @@
+Remark line goes here
+MASS
+
+BOND
+
+ANGLE
+
+DIHE
+
+IMPROPER
+c2-ha-c2-ha 1.1 180.0 2.0 Using the default value
+c2-c2-c2-os 1.1 180.0 2.0 Using the default value
+c2-o -c2-o 1.1 180.0 2.0 Using the default value
+c2-c3-c2-ha 1.1 180.0 2.0 Using the default value
+c2-c2-c2-c2 1.1 180.0 2.0 Using the default value
+c2-c2-c2-ha 1.1 180.0 2.0 Using the default value
+
+NONBON
+
+
+
diff -r 000000000000 -r 2e202f6c3034 test-data/LigA_prmchk.mol2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LigA_prmchk.mol2 Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,59 @@
+@MOLECULE
+MOL
+ 24 24 1 0 0
+SMALL
+bcc
+
+
+@ATOM
+ 1 C 49.2110 26.9920 85.5530 c2 1 MOL -0.412000
+ 2 H 49.1050 28.0330 85.7020 ha 1 MOL 0.190500
+ 3 H1 48.8320 26.6060 84.6410 ha 1 MOL 0.190500
+ 4 C1 49.8460 26.1960 86.4430 c2 1 MOL 0.290000
+ 5 C2 50.0590 24.7460 86.2630 c2 1 MOL 0.448000
+ 6 O 50.4810 24.0440 87.2160 o 1 MOL -0.224000
+ 7 O1 49.8330 24.2110 85.1490 o 1 MOL -0.224000
+ 8 O2 50.3730 26.8140 87.5890 os 1 MOL -0.260000
+ 9 C3 51.7280 27.3660 87.5930 c3 1 MOL -0.040000
+ 10 H2 51.8840 27.9250 88.5040 h1 1 MOL 0.169000
+ 11 C4 51.8170 28.2920 86.3980 c2 1 MOL -0.190000
+ 12 H3 51.3990 29.2560 86.5300 ha 1 MOL 0.188000
+ 13 C5 52.1840 27.8630 85.1670 c2 1 MOL 0.171000
+ 14 C6 52.8190 26.5610 85.0450 c2 1 MOL -0.190000
+ 15 H4 53.0370 26.2220 84.0630 ha 1 MOL 0.188000
+ 16 C7 53.1170 25.8090 86.1190 c2 1 MOL -0.040000
+ 17 H5 53.5700 24.8590 86.0130 ha 1 MOL 0.169000
+ 18 C8 52.7610 26.1980 87.5410 c3 1 MOL -0.003000
+ 19 H6 52.3530 25.3480 88.0710 h1 1 MOL 0.221000
+ 20 O3 54.0020 26.6280 88.1730 oh 1 MOL -0.280000
+ 21 H7 54.4570 27.1880 87.5220 ho 1 MOL 0.215000
+ 22 C9 51.9410 28.6780 83.9640 c2 1 MOL 0.366000
+ 23 O4 51.9100 29.9280 84.0860 o 1 MOL -0.472500
+ 24 O5 51.8570 28.1570 82.8230 o 1 MOL -0.472500
+@BOND
+ 1 1 2 1
+ 2 1 3 1
+ 3 1 4 1
+ 4 4 5 1
+ 5 4 8 1
+ 6 5 6 1
+ 7 5 7 1
+ 8 8 9 1
+ 9 9 10 1
+ 10 9 11 1
+ 11 9 18 1
+ 12 11 12 1
+ 13 11 13 1
+ 14 13 14 1
+ 15 13 22 1
+ 16 14 15 1
+ 17 14 16 1
+ 18 16 17 1
+ 19 16 18 1
+ 20 18 19 1
+ 21 18 20 1
+ 22 20 21 1
+ 23 22 23 1
+ 24 22 24 1
+@SUBSTRUCTURE
+ 1 MOL 1 TEMP 0 **** **** 0 ROOT
diff -r 000000000000 -r 2e202f6c3034 test-data/base_GMX.gro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/base_GMX.gro Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,25 @@
+base6_GMX.gro created by acpype (v: 2018-04-24T22:34:57UTC) on Tue Jun 11 14:15:01 2019
+ 22
+ 1 JZ4 C4 1 0.079 0.137 0.220
+ 1 JZ4 C7 2 0.660 0.042 0.244
+ 1 JZ4 C8 3 0.732 0.091 0.136
+ 1 JZ4 C9 4 0.665 0.133 0.022
+ 1 JZ4 C10 5 0.525 0.126 0.016
+ 1 JZ4 C11 6 0.521 0.034 0.238
+ 1 JZ4 C12 7 0.451 0.077 0.124
+ 1 JZ4 C13 8 0.300 0.067 0.120
+ 1 JZ4 C14 9 0.231 0.148 0.230
+ 1 JZ4 OAB 10 0.460 0.167 -0.097
+ 1 JZ4 H 11 0.032 0.193 0.301
+ 1 JZ4 H1 12 0.047 0.033 0.227
+ 1 JZ4 H2 13 0.043 0.178 0.125
+ 1 JZ4 H3 14 0.712 0.009 0.334
+ 1 JZ4 H4 15 0.840 0.097 0.141
+ 1 JZ4 H5 16 0.722 0.171 -0.062
+ 1 JZ4 H6 17 0.466 -0.006 0.324
+ 1 JZ4 H7 18 0.273 -0.039 0.128
+ 1 JZ4 H8 19 0.262 0.100 0.023
+ 1 JZ4 H9 20 0.260 0.253 0.223
+ 1 JZ4 H10 21 0.262 0.113 0.329
+ 1 JZ4 H11 22 0.526 0.196 -0.162
+ 16.16600 5.85200 9.92000
diff -r 000000000000 -r 2e202f6c3034 test-data/base_GMX.itp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/base_GMX.itp Thu Jun 13 06:16:34 2019 -0400
@@ -0,0 +1,218 @@
+; base_GMX.itp created by acpype (v: 2019-03-22T14:36:00UTC) on Fri May 31 15:21:44 2019
+
+[ atomtypes ]
+;name bond_type mass charge ptype sigma epsilon Amb
+ c3 c3 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094
+ ca ca 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
+ oh oh 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104
+ hc hc 0.00000 0.00000 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157
+ ha ha 0.00000 0.00000 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150
+ ho ho 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
+
+[ moleculetype ]
+;name nrexcl
+ base 3
+
+[ atoms ]
+; nr type resi res atom cgnr charge mass ; qtot bond_type
+ 1 c3 1 JZ4 C4 1 -0.093100 12.01000 ; qtot -0.093
+ 2 ca 1 JZ4 C7 2 -0.162000 12.01000 ; qtot -0.255
+ 3 ca 1 JZ4 C8 3 -0.095000 12.01000 ; qtot -0.350
+ 4 ca 1 JZ4 C9 4 -0.211000 12.01000 ; qtot -0.561
+ 5 ca 1 JZ4 C10 5 0.124100 12.01000 ; qtot -0.437
+ 6 ca 1 JZ4 C11 6 -0.099000 12.01000 ; qtot -0.536
+ 7 ca 1 JZ4 C12 7 -0.098300 12.01000 ; qtot -0.634
+ 8 c3 1 JZ4 C13 8 -0.032100 12.01000 ; qtot -0.666
+ 9 c3 1 JZ4 C14 9 -0.075400 12.01000 ; qtot -0.742
+ 10 oh 1 JZ4 OAB 10 -0.500101 16.00000 ; qtot -1.242
+ 11 hc 1 JZ4 H 11 0.032700 1.00800 ; qtot -1.209
+ 12 hc 1 JZ4 H1 12 0.032700 1.00800 ; qtot -1.177
+ 13 hc 1 JZ4 H2 13 0.032700 1.00800 ; qtot -1.144
+ 14 ha 1 JZ4 H3 14 0.133000 1.00800 ; qtot -1.011
+ 15 ha 1 JZ4 H4 15 0.132000 1.00800 ; qtot -0.879
+ 16 ha 1 JZ4 H5 16 0.132000 1.00800 ; qtot -0.747
+ 17 ha 1 JZ4 H6 17 0.134000 1.00800 ; qtot -0.613
+ 18 hc 1 JZ4 H7 18 0.055700 1.00800 ; qtot -0.557
+ 19 hc 1 JZ4 H8 19 0.055700 1.00800 ; qtot -0.501
+ 20 hc 1 JZ4 H9 20 0.041700 1.00800 ; qtot -0.460
+ 21 hc 1 JZ4 H10 21 0.041700 1.00800 ; qtot -0.418
+ 22 ho 1 JZ4 H11 22 0.418000 1.00800 ; qtot -0.000
+
+[ bonds ]
+; ai aj funct r k
+ 1 9 1 1.5375e-01 2.5179e+05 ; C4 - C14
+ 1 11 1 1.0969e-01 2.7665e+05 ; C4 - H
+ 1 12 1 1.0969e-01 2.7665e+05 ; C4 - H1
+ 1 13 1 1.0969e-01 2.7665e+05 ; C4 - H2
+ 2 3 1 1.3984e-01 3.8585e+05 ; C7 - C8
+ 2 6 1 1.3984e-01 3.8585e+05 ; C7 - C11
+ 2 14 1 1.0860e-01 2.8937e+05 ; C7 - H3
+ 3 4 1 1.3984e-01 3.8585e+05 ; C8 - C9
+ 3 15 1 1.0860e-01 2.8937e+05 ; C8 - H4
+ 4 5 1 1.3984e-01 3.8585e+05 ; C9 - C10
+ 4 16 1 1.0860e-01 2.8937e+05 ; C9 - H5
+ 5 7 1 1.3984e-01 3.8585e+05 ; C10 - C12
+ 5 10 1 1.3637e-01 3.2133e+05 ; C10 - OAB
+ 6 7 1 1.3984e-01 3.8585e+05 ; C11 - C12
+ 6 17 1 1.0860e-01 2.8937e+05 ; C11 - H6
+ 7 8 1 1.5156e-01 2.6861e+05 ; C12 - C13
+ 8 9 1 1.5375e-01 2.5179e+05 ; C13 - C14
+ 8 18 1 1.0969e-01 2.7665e+05 ; C13 - H7
+ 8 19 1 1.0969e-01 2.7665e+05 ; C13 - H8
+ 9 20 1 1.0969e-01 2.7665e+05 ; C14 - H9
+ 9 21 1 1.0969e-01 2.7665e+05 ; C14 - H10
+ 10 22 1 9.7300e-02 3.1079e+05 ; OAB - H11
+
+[ pairs ]
+; ai aj funct
+ 1 7 1 ; C4 - C12
+ 1 18 1 ; C4 - H7
+ 1 19 1 ; C4 - H8
+ 2 5 1 ; C7 - C10
+ 2 8 1 ; C7 - C13
+ 2 16 1 ; C7 - H5
+ 3 7 1 ; C8 - C12
+ 3 10 1 ; C8 - OAB
+ 3 17 1 ; C8 - H6
+ 4 6 1 ; C9 - C11
+ 4 8 1 ; C9 - C13
+ 4 14 1 ; C9 - H3
+ 4 22 1 ; C9 - H11
+ 5 9 1 ; C10 - C14
+ 5 15 1 ; C10 - H4
+ 5 17 1 ; C10 - H6
+ 5 18 1 ; C10 - H7
+ 5 19 1 ; C10 - H8
+ 6 9 1 ; C11 - C14
+ 6 10 1 ; C11 - OAB
+ 6 15 1 ; C11 - H4
+ 6 18 1 ; C11 - H7
+ 6 19 1 ; C11 - H8
+ 7 14 1 ; C12 - H3
+ 7 16 1 ; C12 - H5
+ 7 20 1 ; C12 - H9
+ 7 21 1 ; C12 - H10
+ 7 22 1 ; C12 - H11
+ 8 10 1 ; C13 - OAB
+ 8 17 1 ; C13 - H6
+ 10 16 1 ; OAB - H5
+ 11 8 1 ; H - C13
+ 11 20 1 ; H - H9
+ 11 21 1 ; H - H10
+ 12 8 1 ; H1 - C13
+ 12 20 1 ; H1 - H9
+ 12 21 1 ; H1 - H10
+ 13 8 1 ; H2 - C13
+ 13 20 1 ; H2 - H9
+ 13 21 1 ; H2 - H10
+ 14 15 1 ; H3 - H4
+ 14 17 1 ; H3 - H6
+ 15 16 1 ; H4 - H5
+ 18 20 1 ; H7 - H9
+ 18 21 1 ; H7 - H10
+ 19 20 1 ; H8 - H9
+ 19 21 1 ; H8 - H10
+
+[ angles ]
+; ai aj ak funct theta cth
+ 1 9 8 1 1.1151e+02 5.2635e+02 ; C4 - C14 - C13
+ 1 9 20 1 1.0980e+02 3.8744e+02 ; C4 - C14 - H9
+ 1 9 21 1 1.0980e+02 3.8744e+02 ; C4 - C14 - H10
+ 2 3 4 1 1.2002e+02 5.5731e+02 ; C7 - C8 - C9
+ 2 3 15 1 1.1988e+02 4.0334e+02 ; C7 - C8 - H4
+ 2 6 7 1 1.2002e+02 5.5731e+02 ; C7 - C11 - C12
+ 2 6 17 1 1.1988e+02 4.0334e+02 ; C7 - C11 - H6
+ 3 2 6 1 1.2002e+02 5.5731e+02 ; C8 - C7 - C11
+ 3 2 14 1 1.1988e+02 4.0334e+02 ; C8 - C7 - H3
+ 3 4 5 1 1.2002e+02 5.5731e+02 ; C8 - C9 - C10
+ 3 4 16 1 1.1988e+02 4.0334e+02 ; C8 - C9 - H5
+ 4 3 15 1 1.1988e+02 4.0334e+02 ; C9 - C8 - H4
+ 4 5 7 1 1.2002e+02 5.5731e+02 ; C9 - C10 - C12
+ 4 5 10 1 1.1990e+02 5.8158e+02 ; C9 - C10 - OAB
+ 5 4 16 1 1.1988e+02 4.0334e+02 ; C10 - C9 - H5
+ 5 7 6 1 1.2002e+02 5.5731e+02 ; C10 - C12 - C11
+ 5 7 8 1 1.2077e+02 5.3137e+02 ; C10 - C12 - C13
+ 5 10 22 1 1.0858e+02 4.1003e+02 ; C10 - OAB - H11
+ 6 2 14 1 1.1988e+02 4.0334e+02 ; C11 - C7 - H3
+ 6 7 8 1 1.2077e+02 5.3137e+02 ; C11 - C12 - C13
+ 7 5 10 1 1.1990e+02 5.8158e+02 ; C12 - C10 - OAB
+ 7 6 17 1 1.1988e+02 4.0334e+02 ; C12 - C11 - H6
+ 7 8 9 1 1.1207e+02 5.2802e+02 ; C12 - C13 - C14
+ 7 8 18 1 1.1047e+02 3.9162e+02 ; C12 - C13 - H7
+ 7 8 19 1 1.1047e+02 3.9162e+02 ; C12 - C13 - H8
+ 8 9 20 1 1.0980e+02 3.8744e+02 ; C13 - C14 - H9
+ 8 9 21 1 1.0980e+02 3.8744e+02 ; C13 - C14 - H10
+ 9 1 11 1 1.0980e+02 3.8744e+02 ; C14 - C4 - H
+ 9 1 12 1 1.0980e+02 3.8744e+02 ; C14 - C4 - H1
+ 9 1 13 1 1.0980e+02 3.8744e+02 ; C14 - C4 - H2
+ 9 8 18 1 1.0980e+02 3.8744e+02 ; C14 - C13 - H7
+ 9 8 19 1 1.0980e+02 3.8744e+02 ; C14 - C13 - H8
+ 11 1 12 1 1.0758e+02 3.2970e+02 ; H - C4 - H1
+ 11 1 13 1 1.0758e+02 3.2970e+02 ; H - C4 - H2
+ 12 1 13 1 1.0758e+02 3.2970e+02 ; H1 - C4 - H2
+ 18 8 19 1 1.0758e+02 3.2970e+02 ; H7 - C13 - H8
+ 20 9 21 1 1.0758e+02 3.2970e+02 ; H9 - C14 - H10
+
+[ dihedrals ] ; propers
+; for gromacs 4.5 or higher, using funct 9
+; i j k l func phase kd pn
+ 1 9 8 7 9 0.00 0.65084 3 ; C4- C14- C13- C12
+ 1 9 8 18 9 0.00 0.66944 3 ; C4- C14- C13- H7
+ 1 9 8 19 9 0.00 0.66944 3 ; C4- C14- C13- H8
+ 2 3 4 5 9 180.00 15.16700 2 ; C7- C8- C9- C10
+ 2 3 4 16 9 180.00 15.16700 2 ; C7- C8- C9- H5
+ 2 6 7 5 9 180.00 15.16700 2 ; C7- C11- C12- C10
+ 2 6 7 8 9 180.00 15.16700 2 ; C7- C11- C12- C13
+ 3 2 6 7 9 180.00 15.16700 2 ; C8- C7- C11- C12
+ 3 2 6 17 9 180.00 15.16700 2 ; C8- C7- C11- H6
+ 3 4 5 7 9 180.00 15.16700 2 ; C8- C9- C10- C12
+ 3 4 5 10 9 180.00 15.16700 2 ; C8- C9- C10- OAB
+ 4 3 2 6 9 180.00 15.16700 2 ; C9- C8- C7- C11
+ 4 3 2 14 9 180.00 15.16700 2 ; C9- C8- C7- H3
+ 4 5 7 6 9 180.00 15.16700 2 ; C9- C10- C12- C11
+ 4 5 7 8 9 180.00 15.16700 2 ; C9- C10- C12- C13
+ 4 5 10 22 9 180.00 3.76560 2 ; C9- C10- OAB- H11
+ 5 4 3 15 9 180.00 15.16700 2 ; C10- C9- C8- H4
+ 5 7 6 17 9 180.00 15.16700 2 ; C10- C12- C11- H6
+ 5 7 8 9 9 0.00 0.00000 0 ; C10- C12- C13- C14
+ 5 7 8 18 9 0.00 0.00000 0 ; C10- C12- C13- H7
+ 5 7 8 19 9 0.00 0.00000 0 ; C10- C12- C13- H8
+ 6 2 3 15 9 180.00 15.16700 2 ; C11- C7- C8- H4
+ 6 7 5 10 9 180.00 15.16700 2 ; C11- C12- C10- OAB
+ 6 7 8 9 9 0.00 0.00000 0 ; C11- C12- C13- C14
+ 6 7 8 18 9 0.00 0.00000 0 ; C11- C12- C13- H7
+ 6 7 8 19 9 0.00 0.00000 0 ; C11- C12- C13- H8
+ 7 5 4 16 9 180.00 15.16700 2 ; C12- C10- C9- H5
+ 7 5 10 22 9 180.00 3.76560 2 ; C12- C10- OAB- H11
+ 7 6 2 14 9 180.00 15.16700 2 ; C12- C11- C7- H3
+ 7 8 9 20 9 0.00 0.65084 3 ; C12- C13- C14- H9
+ 7 8 9 21 9 0.00 0.65084 3 ; C12- C13- C14- H10
+ 8 7 5 10 9 180.00 15.16700 2 ; C13- C12- C10- OAB
+ 8 7 6 17 9 180.00 15.16700 2 ; C13- C12- C11- H6
+ 10 5 4 16 9 180.00 15.16700 2 ; OAB- C10- C9- H5
+ 11 1 9 8 9 0.00 0.66944 3 ; H- C4- C14- C13
+ 11 1 9 20 9 0.00 0.62760 3 ; H- C4- C14- H9
+ 11 1 9 21 9 0.00 0.62760 3 ; H- C4- C14- H10
+ 12 1 9 8 9 0.00 0.66944 3 ; H1- C4- C14- C13
+ 12 1 9 20 9 0.00 0.62760 3 ; H1- C4- C14- H9
+ 12 1 9 21 9 0.00 0.62760 3 ; H1- C4- C14- H10
+ 13 1 9 8 9 0.00 0.66944 3 ; H2- C4- C14- C13
+ 13 1 9 20 9 0.00 0.62760 3 ; H2- C4- C14- H9
+ 13 1 9 21 9 0.00 0.62760 3 ; H2- C4- C14- H10
+ 14 2 3 15 9 180.00 15.16700 2 ; H3- C7- C8- H4
+ 14 2 6 17 9 180.00 15.16700 2 ; H3- C7- C11- H6
+ 15 3 4 16 9 180.00 15.16700 2 ; H4- C8- C9- H5
+ 18 8 9 20 9 0.00 0.62760 3 ; H7- C13- C14- H9
+ 18 8 9 21 9 0.00 0.62760 3 ; H7- C13- C14- H10
+ 19 8 9 20 9 0.00 0.62760 3 ; H8- C13- C14- H9
+ 19 8 9 21 9 0.00 0.62760 3 ; H8- C13- C14- H10
+
+[ dihedrals ] ; impropers
+; treated as propers in GROMACS to use correct AMBER analytical function
+; i j k l func phase kd pn
+ 2 4 3 15 4 180.00 4.60240 2 ; C7- C9- C8- H4
+ 2 7 6 17 4 180.00 4.60240 2 ; C7- C12- C11- H6
+ 3 5 4 16 4 180.00 4.60240 2 ; C8- C10- C9- H5
+ 3 6 2 14 4 180.00 4.60240 2 ; C8- C11- C7- H3
+ 4 7 5 10 4 180.00 4.60240 2 ; C9- C12- C10- OAB
+ 5 6 7 8 4 180.00 4.60240 2 ; C10- C11- C12- C13