Mercurial > repos > chemteam > acpype_amber2gromacs
diff test-data/ZAFF.prep @ 1:5b4ae74b7f0b draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit def3e8d4a983ab47ceedde678f585b54c79bb8d1"
| author | chemteam |
|---|---|
| date | Thu, 27 Jan 2022 17:19:05 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ZAFF.prep Thu Jan 27 17:19:05 2022 +0000 @@ -0,0 +1,1015 @@ + 1 1 2 +ZAFF_201108 set created by MTK++/MCPB +CYSTEINE with negative charge + + CY1 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.54300 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.18377 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.18377 + 11 SG S1 E 8 6 4 1.810 116.000 180.000 -0.43963 + 12 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N HN + CA +M C O + +DONE +Zinc(II) Ion + + ZN1 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 ZN ZN M 3 2 1 1.000 90.000 180.000 0.52437 + +DONE +CYSTEINE with negative charge + + CY2 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 + 5 HN H E 4 3 2 1.010 119.800 0.000 0.25200 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03500 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.04800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.42561 + 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.17337 + 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.17337 + 11 SG S2 E 8 6 4 1.810 116.000 180.000 -0.44155 + 12 C C M 6 4 3 1.522 111.100 180.000 0.61600 + 13 O O E 12 6 4 1.229 120.500 0.000 -0.50400 + +IMPROPER + -M CA N HN + CA +M C O + +DONE +HISTIDINE EPSILONH + + HE1 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.04092 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.06506 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.06506 + 11 CG CC S 8 6 4 1.510 115.000 180.000 -0.11300 + 12 ND1 N1 S 11 8 6 1.390 122.000 180.000 -0.08206 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.14656 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.19871 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.01782 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.27163 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.19685 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.12407 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE 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CD2 CV S 16 14 12 1.360 110.000 0.000 0.04659 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.10306 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +Zinc(II) Ion + + ZN5 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 ZN ZN M 3 2 1 1.000 90.000 180.000 0.46992 + +DONE +ASPARTIC ACID + + AP1 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.51630 + 5 H H E 4 3 2 1.010 119.800 0.000 0.29360 + 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03810 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08800 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.24878 + 9 HB2 HC E 8 6 4 1.090 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108.000 180.000 -0.03989 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.17207 + 16 NE2 NR S 14 12 11 1.310 109.000 0.000 -0.09616 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 -0.09905 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.16357 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +Zinc(II) Ion + + Z10 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 ZN ZN M 3 2 1 1.000 90.000 180.000 0.30693 + +DONE +HISTIDINE DELTAH + + HD4 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 + 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 + 6 CA CT M 4 3 2 1.449 121.900 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CT M 4 3 2 1.449 121.900 180.000 0.01880 + 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08810 + 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.74837 + 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.11954 + 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.11954 + 11 CG CC S 8 6 4 1.510 115.000 180.000 -0.41256 + 12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.12169 + 13 HD1 H E 12 11 8 1.010 126.000 0.000 0.32152 + 14 CE1 CR B 12 11 8 1.320 108.000 180.000 0.15077 + 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.16196 + 16 NE2 NT S 14 12 11 1.310 109.000 0.000 -0.61460 + 17 CD2 CV S 16 14 12 1.360 110.000 0.000 0.33532 + 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.01604 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CG CE1 ND1 HD1 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +WATER, TIP3P MODEL + + WT2 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 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1.510 115.000 180.000 -0.28845 + 12 ND1 NY S 11 8 6 1.390 122.000 180.000 -0.49024 + 13 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.00101 + 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.15620 + 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.04727 + 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.34231 + 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.12203 + 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.26454 + 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 + 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 + +LOOP + CG CD2 + +IMPROPER + -M CA N H + CA +M C O + CE1 CD2 NE2 HE2 + CG NE2 CD2 HD2 + ND1 NE2 CE1 HE1 + ND1 CD2 CG CB + +DONE +WATER, TIP3P MODEL + + WT3 INT 1 + CORR OMIT DU BEG +0.00000 + 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000 + 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000 + 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000 + 4 H1 HW M 3 2 1 1.000 101.430 -98.890 0.40063 + 5 O O4 M 4 3 2 0.957 104.520 -39.220 -0.60020 + 6 H2 HW E 5 4 3 0.957 104.520 -151.000 0.40063 + +LOOP + H1 H2 + +DONE +Zinc(II) Ion + + Z12 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