ReactionMechanismGenerator / ReactionMechanismGenerator/ARC

Force field conformer generated by ARC has atoms too close to each other

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#381 0 comments 0 reactions 1 assignee View on GitHub

@alongd is already working on this.

Since Apr 18, 2020.

Type: Bug
Dominant language
Python
Stars
51
Forks
25
Avg merge
4d 5h
Merged PRs (30d)
15

Description

Describe the bug
Force field conformer generated by ARC has atoms too close to each other
Screenshot_20200417_180410

How to reproduce
Species smile: [O]OCN(C(CCN1C2C=CC=CC=2CCC2=C1C=CC=C2)OO)C
Species xyz:
0 2
O 5.98370000 0.37132000 0.46074000
O 5.70019000 -0.58273000 -0.54099000
C 4.89638000 0.08236000 -1.53025000
N 3.47911000 -0.32753000 -1.58480000
C 2.75429000 0.12718000 -0.38202000
C 1.23215000 -0.04819000 -0.51236000
C 0.50213000 0.59642000 0.67840000
N 0.63095199 -0.22176957 1.91046465
C 1.91775900 -0.44150718 2.46475683
C 2.93204116 0.53225871 2.28433134
C 4.21492887 0.40509149 2.82465662
C 4.52931847 -0.70313101 3.58772941
C 3.55910549 -1.67610048 3.79821252
C 2.26000874 -1.57330963 3.23938139
C 1.34230800 -2.73703090 3.55623530
C 0.17198268 -2.97584869 2.61259074
C -0.88117179 -1.92739539 2.82622894
C -0.60860500 -0.59605047 2.48293610
C -1.60503399 0.36726902 2.72838932
C -2.83907055 0.01721923 3.28052924
C -3.10010228 -1.30875490 3.60302411
C -2.12492120 -2.27788511 3.38009565
O 3.18162000 -0.57639000 0.79475000
O 3.61429000 0.43375000 1.75761000
C 3.36444000 -1.76545000 -1.82144000
H 5.35957000 -0.14014000 -2.49930000
H 4.97056000 1.17379000 -1.42745000
H 2.94372000 1.20385000 -0.26734000
H 0.87508000 0.40834000 -1.44429000
H 0.98694000 -1.11327000 -0.55965000
H -0.54952307 0.69051069 0.37359323
H 0.83474295 1.62168646 0.87168515
H 2.73463317 1.44500815 1.72908443
H 4.95321941 1.18400765 2.65664949
H 5.51805753 -0.81002778 4.02364674
H 3.81837557 -2.54017643 4.40836142
H 0.98296633 -2.61552897 4.58698686
H 1.94613530 -3.65503546 3.53781130
H -0.24918518 -3.96835316 2.81672544
H 0.48954951 -2.98882076 1.56263967
H -1.41153777 1.41478581 2.51035066
H -3.58756991 0.78273301 3.46496066
H -4.05633257 -1.58710101 4.03728002
H -2.33487495 -3.31048390 3.64871419
H 4.57563000 0.38668000 1.54970000
H 3.83868749 -2.33937731 -1.01950162
H 2.31118150 -2.06982729 -1.81935035
H 3.80130490 -2.07692004 -2.77652275

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