;----------------------------TITLE ----------------------------------------------------------------------------------------- ; Ethanol ; ; This file was generated at 23:32 on 2022-06-15 by ; ; Automatic Topology Builder ; ; REVISION 2022-06-14 23:25:45 ;--------------------------------------------------------------------------------------------------------------------------- ; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark ; ; Institute : Molecular Dynamics group, ; School of Chemistry and Molecular Biosciences (SCMB), ; The University of Queensland, QLD 4072, Australia ; URL : https://atb.uq.edu.au ; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. ; An Automated force field Topology Builder (ATB) and repository: version 1.0. ; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. ; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. ; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. ; DOI:10.1021/acs.jctc.8b00768 ; ; Disclaimer : ; While every effort has been made to ensure the accuracy and validity of parameters provided below ; the assignment of parameters is being based on an automated procedure combining data provided by a ; given user as well as calculations performed using third party software. They are provided as a guide. ; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided ; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion ; and to perform additional validation tests for their specific application if required. Neither the authors ; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. ; ; Release notes and warnings: ; (1) The topology is based on a set of atomic coordinates and other data provided by the user after ; after quantum mechanical optimization of the structure using different levels of theory depending on ; the nature of the molecule. ; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. ; In these cases alternative type codes are provided at the end of the line. ; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral ; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" ; or "uncertain" in comments. ; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder ; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually ; before the file can be used. ;--------------------------------------------------------------------------------------------------------------------------- ; Input Structure : BIPQ ; Output : ALL ATOM topology ; Use in conjunction with the corresponding all atom PDB file. ;--------------------------------------------------------------------------------------------------------------------------- ; Citing this topology file ; ATB molid: 902261 ; ATB Topology Hash: 25be5 ;--------------------------------------------------------------------------------------------------------------------------- ; Final Topology Generation was performed using: ; A B3LYP/6-31G* optimized geometry. ; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. ; Initial charges were estimated using the ESP method of Merz-Kollman. ; Final charges and charge groups were generated by method described in the ATB paper. ; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. ;--------------------------------------------------------------------------------------------------------------------------- ; ; [ moleculetype ] ; Name nrexcl BIPQ 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 HS14 1 BIPQ H6 1 0.427 1.0080 2 OAlc 1 BIPQ O1 2 -0.704 15.9994 3 CPos 1 BIPQ C2 3 0.381 12.0110 4 HC 1 BIPQ H4 4 -0.011 1.0080 5 HC 1 BIPQ H5 5 -0.011 1.0080 6 C 1 BIPQ C1 6 -0.319 12.0110 7 HC 1 BIPQ H1 7 0.079 1.0080 8 HC 1 BIPQ H2 8 0.079 1.0080 9 HC 1 BIPQ H3 9 0.079 1.0080 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 2 2 0.0972 1.9581e+07 2 3 2 0.1430 8.1800e+06 3 4 2 0.1090 1.2300e+07 3 5 2 0.1090 1.2300e+07 3 6 2 0.1530 7.1500e+06 6 7 2 0.1090 1.2300e+07 6 8 2 0.1090 1.2300e+07 6 9 2 0.1090 1.2300e+07 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 1 4 1 1 5 1 1 6 1 2 7 1 2 8 1 2 9 1 4 7 1 4 8 1 4 9 1 5 7 1 5 8 1 5 9 1 [ angles ] ; ai aj ak funct angle fc 1 2 3 2 109.50 450.00 2 3 4 2 110.30 524.00 2 3 5 2 110.30 524.00 2 3 6 2 111.00 530.00 4 3 5 2 107.57 484.00 4 3 6 2 110.30 524.00 5 3 6 2 110.30 524.00 3 6 7 2 111.00 530.00 3 6 8 2 111.00 530.00 3 6 9 2 111.00 530.00 7 6 8 2 108.53 443.00 7 6 9 2 108.53 443.00 8 6 9 2 108.53 443.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc [ dihedrals ] ; ai aj ak al funct ph0 cp mult 1 2 3 6 1 0.00 1.26 3 2 3 6 7 1 0.00 5.92 3 [ exclusions ] ; ai aj funct ; GROMOS 1-4 exclusions