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Recent changes:

  • The ATB has been recently update, details on the changes from version 1.2 are available here.
  • Due to minor changes to the ATBs bonded parameter assignment, the GROMOS parameter files generated by the ATB (IFP files) have been updated.
    Topologies generated previously are not compatible with the latest IFP file and vice versa.
    GROMACS compatible files are unaffected.
  • Version 2.1 updates include: greater pipeline stability, improved atom ordering, and minor changes to bonded parameter assignment.

ATB 2.0 validation study:

  • Koziara KB, Stroet M, Malde AK, Mark AE.
    Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
    Journal of Computer-Aided Molecular Design, 2014.
    DOI:10.1007/s10822-014-9713-7

The improved charge group assignment used for 2.0 topologies is described in:

  • Canzar S, El-Kebir M, Pool R, Elbassioni K, Malde AK, Mark AE, Geerke DP, Stougie L, Klau GW.
    Charge Group Partitioning in Biomolecular Simulation.
    Journal of Computational Biology, 2013, 20, 188-198.
    DOI:10.1089/cmb.2012.0239

The ATB paper is now available:

  • 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(12), 4026-4037.
    DOI: 10.1021/ct200196m

Latest ATB forcefield files

GROMOS 54A7 IFP files with additions from the ATB:

GROMOS 53A6 IFP files with additions from the ATB:

Overview

The ATB and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include:

  • The study of biomolecule:ligand complexes
  • Free energy calculations
  • Structure-based drug design
  • The refinement of x-ray crystal complexes

This site provides:

  • A repository for building blocks and interaction parameter files for molecules described using GROMOS force fields.
  • An automated builder to help generate building blocks for novel molecules, compatible with the GROMOS 53A6 force field and in formats appropriate for the GROMACS, GROMOS simulation packages and CNS, Phenix, CCP4 and Refmac5 X-ray refinement packages.
  • Refined geometries for molecules within the repository.
  • Equilibrated starting coordinates for a range of biologically important systems.

Getting started

See the FAQ page to get started.

Tutorials for common tasks on the ATB are currently being developed, the first of which is available here: How to View an Existing Molecule

Disclaimer
While every effort has been made to provide reliable estimates of the parameters including where appropriate alternative choices of parameters, these are intended as a guide. The user should carefully examine all files before use and the suitability of the parameters provided for any specific application cannot be guaranteed.

Submit

If you have previously submitted a molecule with ATB, but have not received a password,please go here to generate a password.


  You must be registered and logged in to submit a molecule! Please either login or register.

Existing Molecules

Overall Statistics
Molecule TypeManual (Highly Trusted) Manual ATB
amino acid 1 204 196
amino acid building block 61 205 0
heteromolecule 61 13 10816
lipid 56 6 215
nucleic acid 0 1 24
solvent 8 0 52
sugar 14 0 193
sugar building block 3 0 0

Total molecules: 12129
Search
Search string*:
Molecule type:
Curation:
* The search string is matched to IUPAC Name,
  Common Name/Description, Residue Name,
  Formula and Canonical SMILES
Selected Molecules (12180)
Page: of 122
Display:
Molecule ID Formula IUPAC Name Common Name/Description Atoms Charge Forcefield Submission Date FilesCuration
21758 C2H3N acetonitrile 5 -1 multiple 2014-11-01 Link Partial
21755 CH4S methanethiol 5 -1 multiple 2014-10-31 Link ATB
21753 C2H6 ethane 7 -1 multiple 2014-10-31 Link ATB
21752 C15H12N2O2 (4Z)-4-[(1-methyl-1H-pyrrol-2- ... unk 31 0 multiple 2014-10-31 Link Partial
21751 C117H224N12O22 2-{N-[(2S)-2-ethylhexyl]-2-{N- ... 375 0 multiple 2014-10-31 Link Partial
21750 C112H214N12O37 2-{N-[(2R)-2-ethylhexyl]-2-{N- ... 375 0 multiple 2014-10-31 Link Partial
21749 C58H112N6O13 2-{N-[(2R)-2-ethylhexyl]-2-{N- ... 189 0 multiple 2014-10-31 Link ATB
21748 C59H114N6O10 2-{N-[(2R)-2-ethylhexyl]-2-{N- ... 189 0 multiple 2014-10-31 Link ATB
21747 C116H222N12O25 2-{N-[(2S)-2-ethylhexyl]-2-{N- ... 375 0 multiple 2014-10-31 Link Partial
21746 C12H16F3N ethyl[(2S)-1-[3-(trifluorometh ... sffH2 33 1 multiple 2014-10-31 Link Partial
21745 C12H16F3N ethyl[(2S)-1-[3-(trifluorometh ... sff 32 0 multiple 2014-10-31 Link Partial
21744 C5H10N2O3 (2R)-2-amino-3-(methylcarbamoy ... N-methyl-D-asparagine 20 0 multiple 2014-10-30 Link ATB
21743 C4H9NO3 (2R,3R)-2-amino-3-hydroxybutan ... D-allothreonine 17 0 multiple 2014-10-30 Link ATB
21742 C42H62O16 (2S,3S,4S,5R,6R)-6-{[(3S,4aR,6 ... Glycyrrhizin from crystal data 120 0 multiple 2014-10-30 Link ATB
21741 C6H12N2O3 (2S,3S)-2-amino-4-carbamoyl-3- ... L-beta-Methylglutamine 23 0 multiple 2014-10-30 Link ATB
21740 C5H11NO3 (2S)-2-amino-3-hydroxy-3-methy ... 3-hydroxyvaline L 20 0 multiple 2014-10-30 Link ATB
21739 C10H15N5O10P2 {[(R)-{[(2R,3S,4R,5R)-5-(6-ami ... ADP_GS 39 -3 multiple 2014-10-30 Link Partial
21738 C22H30N6O4S 5-[2-ethoxy-5-(4-methylpiperaz ... viagra_ting 63 0 multiple 2014-10-30 Link ATB
21737 C58H112N6O13 2-{N-[(2R)-2-ethylhexyl]-2-{N- ... 189 0 multiple 2014-10-30 Link ATB
21736 C112H214N12O37 2-{N-[(2R)-2-ethylhexyl]-2-{N- ... 375 0 multiple 2014-10-30 Link Partial
21735 C117H224N12O22 2-{N-[(2S)-2-ethylhexyl]-2-{N- ... 375 0 multiple 2014-10-30 Link Partial
21734 C116H222N12O25 2-{N-[(2S)-2-ethylhexyl]-2-{N- ... 375 0 multiple 2014-10-30 Link Partial
21733 C33H58O9S (12S)-12-hydroxy-1-{3-[(8E)-pe ... three 100 -1 multiple 2014-10-30 Link ATB
21732 C18H34O3 (9Z,12R)-12-hydroxyoctadec-9-e ... bimayou_ting 55 0 multiple 2014-10-30 Link ATB
21731 C2H3N acetonitrile acetonitrile 6 0 multiple 2014-10-30 Link ATB
21729 C50H27 5_benzene_rings_v2 70 0 multiple 2014-10-30 Link ATB
21728 C30H20 hexacyclo[16.2.2.22,5.2 ... 5_benzene_rings 50 0 multiple 2014-10-30 Link Partial
21725 C6H6 benzene benzene 12 0 multiple 2014-10-30 Link ATB
21724 C9H19O11P [(2S)-2,3-dihydroxypropoxy]({[ ... PO4 40 0 multiple 2014-10-30 Link Partial
21723 C36H11O6S12.H 6_bearing 66 0 multiple 2014-10-30 Link ATB
21722 C42H56O14Si28 14_sleeve 140 0 multiple 2014-10-30 Link ATB
21721 C25H31F3O5S (1R,2S,8S,10S,11S,13R,14R,15S, ... fluticasone propionate 65 0 multiple 2014-10-30 Link ATB
21719 C13H21NO3 4-[(1S)-2-(tert-butylamino)-1- ... salbutamol 38 0 multiple 2014-10-30 Link Partial
21718 C7H8O2 2-methoxybenzen-1-olate Guaiacol 17 0 multiple 2014-10-30 Link ATB
21717 C7H6O5 Gallic Acid 17 -1 multiple 2014-10-30 Link ATB
21716 C22H18O11 5-[(2R,3R)-5,7-dioxido-3-[(3,4 ... EGCG 51 0 multiple 2014-10-30 Link ATB
21715 C6H14O2 (4R)-2-methylpentane-2,4-diol MPD 22 0 multiple 2014-10-29 Link ATB
21713 C9H4O (6S)-6-(prop-1-yn-1-yl)cyclohe ... no 10 0 multiple 2014-10-29 Link ATB
21712 C80H156O4 (2S)-2-[(2E)-2,4,4,6,6,8,8,10, ... pibsa 240 0 multiple 2014-10-29 Link ATB
21711 C77H152N4O2 (3R)-1-[2-({2-[(2-aminoethyl)a ... pibsapam 235 0 multiple 2014-10-29 Link ATB
21709 C36H73NO8P (2R)-1-{[(2S)-2-hydroxy-6,6-di ... DMPC_mono 118 0 multiple 2014-10-29 Link ATB
21707 C6H13NO2 (2R)-2-amino-3,3-dimethylbutan ... D-tert-leucine 22 0 multiple 2014-10-29 Link ATB
21706 C27H50O6 1,3-bis(octanoyloxy)propan-2-y ... mct 83 0 multiple 2014-10-29 Link ATB
21703 H3NO3 5 0 multiple 2014-10-29 Link ATB
21702 C9H6O2 2H-chromen-2-one 17 0 multiple 2014-10-28 Link ATB
21701 C8H18O 1-butoxybutane dibutylether 27 0 multiple 2014-10-28 Link ATB
21700 C52H78O38 Glycerol Succinic OH 2 168 0 multiple 2014-10-28 Link ATB
21697 C16H12ClF3N4O4 4-chloro-5-(dihydroxymethyl)-N ... nilotinib modified 40 0 multiple 2014-10-28 Link Partial
21694 C4H8N8O8 1,3,5,7-tetranitro-1,3,5,7-tet ... g-HMX 28 0 multiple 2014-10-28 Link ATB
21693 C21H22ClNO5 (4R)-2-(2-chlorophenyl)-4-hydr ... 50 0 multiple 2014-10-28 Link ATB
21692 C21H22ClNO5 (4R)-2-(2-chlorophenyl)-4-hydr ... 50 0 multiple 2014-10-28 Link ATB
21691 C8H8O2 2,6-dimethylcyclohexa-2,5-dien ... dim-BQ2 18 0 multiple 2014-10-28 Link ATB
21690 C6H4O2 cyclohexa-2,5-diene-1,4-dione BQ_NEW 12 0 multiple 2014-10-28 Link ATB
21688 C48H62O36 Glycerol Succinic Acid 140 -6 multiple 2014-10-28 Link ATB
21687 C52H80O38 Glycerol Succinic OH 170 0 multiple 2014-10-28 Link ATB
21686 C48H78O28 Glycerol Adipic OH 154 0 multiple 2014-10-28 Link ATB
21684 C6H13NO2 (2S)-2-amino-3,3-dimethylbutan ... 3-Methyl.L-valin 22 0 multiple 2014-10-27 Link ATB
21683 C20H14N2O2 1-amino-4-(phenylamino)-9,10-d ... L9_max 38 0 multiple 2014-10-27 Link ATB
21682 C20H14N2O2 1-amino-4-(phenylamino)-9,10-d ... L9_min 38 0 multiple 2014-10-27 Link ATB
21681 C11H11N5O6S2 3-({[(4-methoxy-6-methyl-1,3,5 ... L8_max 35 0 multiple 2014-10-27 Link ATB
21680 C11H11N5O6S2 3-({[(4-methoxy-6-methyl-1,3,5 ... L8_min 35 0 multiple 2014-10-27 Link ATB
21679 C14H15N5O6S methyl 2-({[(4-methoxy-6-methy ... L7_max 41 0 multiple 2014-10-27 Link ATB
21678 C14H15N5O6S methyl 2-({[(4-methoxy-6-methy ... L7_min 41 0 multiple 2014-10-27 Link ATB
21677 C15H15ClN4O6S ethyl 2-({[(4-chloro-6-methoxy ... L6_max 42 0 multiple 2014-10-27 Link ATB
21676 C15H15ClN4O6S ethyl 2-({[(4-chloro-6-methoxy ... L6_min 42 0 multiple 2014-10-27 Link ATB
21675 C15H16N4O7S 2-[({[(4,6-dimethoxypyrimidin- ... L5_max 43 0 multiple 2014-10-27 Link ATB
21674 C15H16N4O7S 2-[({[(4,6-dimethoxypyrimidin- ... L5_min 43 0 multiple 2014-10-27 Link ATB
21673 C3H6N2O6 (4S)-4-methyl-2,7-dioxo-1,3,6, ... L4_max 17 0 multiple 2014-10-27 Link ATB
21672 C3H6N2O6 (4R)-4-methyl-2,7-dioxo-1,3,6, ... L4_min 17 0 multiple 2014-10-27 Link ATB
21671 C14H10F3NO2 2-{[3-(trifluoromethyl)phenyl] ... L3_max 30 0 multiple 2014-10-27 Link ATB
21670 C14H10F3NO2 2-{[3-(trifluoromethyl)phenyl] ... L3_min 30 0 multiple 2014-10-27 Link ATB
21669 C14H20O2 2,6-di-tert-butylcyclohexa-2,5 ... 2,6-db-BQ 36 0 multiple 2014-10-27 Link ATB
21668 C14H20O2 2,5-di-tert-butylcyclohexa-2,5 ... 2,5-db-BQ 36 0 multiple 2014-10-27 Link ATB
21667 C10H12O2 tetramethylcyclohexa-2,5-diene ... tMe-BQ 24 0 multiple 2014-10-27 Link ATB
21666 C8H8O2 2,6-dimethylcyclohexa-2,5-dien ... 2,6-dim-BQ 18 0 multiple 2014-10-27 Link ATB
21665 C10H12O2 2-tert-butylcyclohexa-2,5-dien ... tBu-BQ 24 0 multiple 2014-10-27 Link ATB
21664 C7H6O2 2-methylcyclohexa-2,5-diene-1, ... Me-BQ 15 0 multiple 2014-10-27 Link ATB
21662 C9H20 (4S)-2,4-dimethylheptane N1-28 28 -1 multiple 2014-10-27 Link ATB
21661 C10H22 2,4,6-trimethylheptane N1-31 31 -1 multiple 2014-10-27 Link ATB
21660 C9H14N5O7P [(2S)-2-[(2-amino-6-oxo-6,9-di ... GCV 36 0 multiple 2014-10-27 Link ATB
21658 C51H86O7 (2S)-3-{[(2R,4aS,6aR,6bS,8aR,1 ... sassmbly 144 0 multiple 2014-10-26 Link ATB
21657 C28H22O6 5-[(2R,3R)-5-[(E)-2-(3,5-dioxi ... T_RR-2 56 0 multiple 2014-10-26 Link ATB
21656 C28H22O6 5-[(2S,3S)-5-[(E)-2-(3,5-dioxi ... T_SS-2 56 0 multiple 2014-10-26 Link ATB
21655 C28H22O6 5-[(2R,3R)-5-[(E)-2-(3,5-dioxi ... T_RR-1 56 0 multiple 2014-10-26 Link ATB
21652 C28H22O6 5-[(2S,3S)-5-[(E)-2-(3,5-dioxi ... T_SS-1 56 0 multiple 2014-10-26 Link ATB
21650 C28H22O6 5-[(2S,3S)-5-[(E)-2-(3,5-dioxi ... R_SS 56 0 multiple 2014-10-26 Link ATB
21649 C28H22O6 5-[(2R,3R)-5-[(E)-2-(3,5-dioxi ... R_RR 56 0 multiple 2014-10-26 Link ATB
21646 C14H24O2 (2R,5R)-2,5-di-tert-butylcyclo ... 3,5-Di-tert-butyl-o-benzoquino ... 40 0 multiple 2014-10-25 Link ATB
21645 C14H24O2 (2R,6S)-2,6-di-tert-butylcyclo ... 2,6-Di-tert-butyl-1,4-benzoqui ... 40 0 multiple 2014-10-25 Link ATB
21644 C8H12O2 (2R,6S)-2,6-dimethylcyclohexan ... 2,5-Dimethyl-1,4-benzoquinone 22 0 multiple 2014-10-25 Link ATB
21643 C7H10O2 (2S)-2-methylcyclohexane-1,4-d ... 2-methyl-1,4-benzoquinone 19 0 multiple 2014-10-25 Link ATB
21642 C6H8O2 cyclohexane-1,4-dione Benzoquinone 16 0 multiple 2014-10-25 Link ATB
21641 C10H16O2 (2R,3S,5R,6S)-2,3,5,6-tetramet ... 2,3,5,6-Tetramethyl-1,4-benzo ... 28 0 multiple 2014-10-25 Link ATB
21640 C10H16O2 (2R)-2-tert-butylcyclohexane-1 ... 28 0 multiple 2014-10-25 Link ATB
21638 C24H20N4O7 54 -1 multiple 2014-10-25 Link ATB
21637 C15H23N6O5S 50 1 multiple 2014-10-25 Link ATB
21636 C66H98O36 Glycerol Adipic acid 194 -6 multiple 2014-10-25 Link ATB
21634 C28H22O6 5-[(2R,3R)-5-[(E)-2-(3,5-dioxi ... 56 0 multiple 2014-10-25 Link ATB
21633 C10H22O4S (decyloxy)sulfonic acid Sodium Decyl Sulfate SDeS 36 -1 multiple 2014-10-25 Link ATB
21632 C12H26O4S (dodecyloxy)sulfonic acid anionic SDS C12H25SO4- 42 -1 multiple 2014-10-25 Link ATB
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Pre-Equilibrated Systems

Pre-Equilibrated Systems in Various Phases

NameDescriptionTemperature (K) Pressure (Bar)Equilibration time (ns)Time step (ps) ProgramBoxReference
512 methanol Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 ethanol Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 ethane amine Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 ethane-1,2-diamine Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 diethylamine Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
343 diethylether Rectangular box; 343 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 butylamine Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 2-propanol Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 aceton Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 acetic acid Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 methyl ethyl ester Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 N-methylacetamide Rectangular box; 512 molecules 301.0 1.013 0.5 0.002 gromos96 Link Link
512 ethyl acetate Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 3-pentanon Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
343 toluene Rectangular box; 343 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 propyl acetate Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 ethylpropanoate Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 ethylbutanoate Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 butyl acetate Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 ethyl glycol dipropanoate Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 glycerol tripropanoate Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
512 Cyclohexane Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 GROMOS96 Link Link
DLPC bilayer Hydrated 128-DLPC bilayer 303.0 1.0 350.0 0.002 GROMACS 3.2.1 Link Link
DLPC bilayer Hydrated 128-DLPC bilayer 303.0 1.0 350.0 0.002 GROMACS 3.2.1 Link Link
DMPC bilayer Hydrated 128-DMPC bilayer 303.0 1.0 235.0 0.002 GROMACS 3.2.1 Link Link
DOPC bilayer Hydrated 128-DOPC bilayer 303.0 1.0 300.0 0.002 GROMACS 3.2.1 Link Link
POPC bilayer Hydrated 128-POPC bilayer 303.0 1.0 250.0 0.002 GROMACS 3.2.1 Link Link
DPPC bilayer Hydrated 128-DPPC bilayer 323.0 1.0 190.0 0.002 GROMACS 3.2.1 Link Link
50 Perc Vol TFE TFE and water volume 1:1, mola ... 0.0 1.0 2.0 0.0 GROMACS 3.3.3 mdrun Link See page
DPC micelle DPC micelle composed of 56 lip ... 0.0 1.0 0.0 0.0 GROMACS 3.3.3 mdrun Link See page
1000 Chloroform Rectangular box; 1000 molecule ... 0.0 1.013 3.0 0.002 gromos96 Link Link
1000 Methanol Rectangular box; 1000 molecule ... 0.0 1.013 2.0 0.002 gromos96 Link Link
1000 Carbon tetrachloride Rectangular box; 1000 molecule ... 0.0 1.013 5.5 0.002 gromos96 Link Link
1024 DMSO Rectangular box; 1024 molecule ... 0.0 1.013 1.0 0.002 gromos96 Link Link
512 Dimethylether Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 2-methyl-2-butanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 2-methyl-2-propanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 cyclohexanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 octanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 heptanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 2-butanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 2-pentanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 3-pentanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 hexanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 pentanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 butanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 (2-propanol) Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 (1-propanol) Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 ethanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
512 methanol Rectangular box; 512 molecules 298.15 1.013 2.0 0.002 gromos96 Link Link
DPPC bilayer Hydrated 128-DPPC bilayer 350.0 1.0 100.0 0.002 GROMACS 3.3.3 Link See page
DPPC bilayer 128-DPPC bilayer in 2.5 mol. % ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DPPC bilayer 128-DPPC bilayer in 5.0 mol. % ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DPPC bilayer 128-DPPC bilayer in 10.0 mol. ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DPPC bilayer 128-DPPC bilayer in 12.5 mol. ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DOPC Hydrated 128-DOPC bilayer 350.0 1.0 100.0 0.002 GROMACS 3.3.3 Link See page
DOPC bilayer 128-DOPC bilayer in 2.5 mol. % ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DOPC bilayer 128-DOPC bilayer in 5.0 mol. % ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DOPC bilayer 128-DOPC bilayer in 10.0 mol. ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DOPC bilayer 128-DOPC bilayer in 12.5 mol. ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
DOPC bilayer 128-DOPC bilayer in 15.0 mol. ... 350.0 1.0 300.0 0.002 GROMACS 3.3.3 Link See page
Membrane-embedded P-glycoprote ... central P-gp structure from 30 ... 300.0 1.0 300.0 0.004 gromacs 3.3.3 mdrun Link Link
P-gp with NCP, ATP in a Choles ... P-gp with NCP, ATP in a Choles ... 0.0 1.0 5.0 0.004 gromacs 3.3.3 mdrun Link See page
512 acetone Rectangular box; 512 molecules 298.15 1.013 0.5 0.002 gromos96 Link Link
Vancomycin and lipid II forms ... Vancomycin spontenoursly attac ... 298.0 1.0 50.0 4.0 GROMACS 4.0.2 Link Link
ATP-bound P-gp inward facing, ... P-gp with Mg2+ and ATP in a PO ... 300.0 1.0 10.0 0.004 GROMACS 3.3.3 Link Link
Membrane-embedded P-gp with AT ... P-gp with Mg2+ and ATP in a PO ... 0.0 0.0 0.0 0.0 GROMACS 3.3.3 Link See page
ATP-bound P-gp asymmetric memb ... P-gp with Mg2+ and ATP in a PO ... 0.0 0.0 0.0 0.0 GROMACS 3.3.3 Link See page
ATP-bound P-gp asymmetric memb ... P-gp with Mg2+ and ATP in a PO ... 0.0 0.0 0.0 0.0 GROMACS 3.3.3 Link See page
Lipid II in POPC membrane System contain 3 lipid II and ... 310.0 1.0 10.0 4.0 GROMACS 4.0.7 Link Link

GROMOS Forcefield Files

The GROMOS Force Field Files

A draft description of the GROMOS force field by the IGC group at ETH, Zurich is given here. The literature reference for the GROMOS 53A6 force field is here.

GROMOS 53A6 IFP files with additions from the ATB
GROMOS11 54a7 ATB.ifp
GROMOS11 53a6 ATB.ifp
GROMOS96 ifp54a7 ATB.dat
GROMOS96 ifp53a6 ATB.dat

GROMOS FF for the GROMACS program
GROMOS54A7_for_Gromacs_3.x_4.0.x.tar.gz GROMOS54A7_for_Gromacs_4.5.x.tar.gz

Additional GROMOS forcefield files can be found here.

GROMOS Manual Preview Chapters
Preview - Manual (Vol. 2) - General Algorithms and Formulae
Preview - Manual (Vol. 3) - Force Field and Topology Data Set
Preview - Manual (Vol. 4) - Data Structures and Formats
Preview - Manual (Vol. 5) - Program Library Manual
Preview - Manual (Vol. 6) - GROMOS Technical Details

Validation

Automated Topology Builder Validation Statistics

Automated Topology Builder Validation Statistics

Automated Topology Builder version 2.0 is validated against structural and thermodynamical data. Validation against root-mean-square deviation and hydration free energies was performed.

Root Mean Square Deviation

In vacuum

As an initial validation of the topologies and parameters generated by the ATB 2.0, each molecule was energy minimized in vacuum and the resulting structure was compared to that obtained after Quantum Mechanical (QM) optimization in implicit solvent (water) at the B3LYP/6-31G* level (≤ 50 atoms) or at the HF/STO-3G level of theory (>50 atoms) using GAMESS-US [1].

An analysis of the root mean square deviation (RMSD) after performing a least squares fit on all atoms for a total of 3310 molecules in the database on the 1-3-2013 is presented below. The number of atoms in the molecules varied from 4 to 659. The molecular weights ranged from 17 to 4453 atomic units. The molecules considered contained carbon, hydrogen, oxygen, silicon, sulphur, phosphorus, nitrogen and halogens (chlorine, bromide, fluorine) and included amino acids, heteromolecules, lipids, nucleic acids, solvents and sugars. RMSD values range from 0.0 to 0.09 nm.

Fig.1. Distribution of RMSD values between QM and energy minimized structures in vacuum.

From the distribution of values in Fig.1, it can be seen that 50% of molecules have an RMSD value below 0.01 nm and almost 95% have an RMSD value below 0.03 nm. Overall the agreement between the QM optimized structures and the energy minimized structures using the ATB parameters is very good which suggests that the geometry of the molecules is well maintained.

In water

To further validate the topologies a test set consisting of 178 heteromolecules was simulated for 200 ps in SPC [2] water at 300K and at 1 atm using the GROMOS11 [3] Molecular Dynamics (MD) simulation package. An analysis of the RMSD of the final structure from the simulations with respect to the structure optimised quantum mechanically was calculated after performing a least squares fit on all atoms. The number of atoms in the molecules varied from 6 to 40. The molecular weights ranged from 28 to 410 atomic units. Again, the molecules considered contained carbon, hydrogen, oxygen, sulphur, phosphorus, nitrogen and halogens (chlorine, bromide, fluorine). The topologies were generated on the 1-3-2013 using the ATB version 2.0

From the distribution of values shown in Fig.2 it can be seen that 50% of molecules have an RMSD value ≤ 0.1 nm with ~95% having an RMSD value ≤ 0.2 nm. Note, these values correspond to a single configuration taken at the end of the simulation. The RMSD values therefore reflect fluctuations due to thermal motion at 300K including the effects of dihedral transitions. The test set included a number of highly flexible and/or hydrophobic molecules such as long aliphatic chains. This explained why a small proportion of molecules show large deviations from the QM optimised structures when simulated in water.


Fig.2. Percentage distribution of RMSD values for 178 molecules (MD)

Hydration Free Energies

The ability of the force field descriptions generated by the ATB 2.0 to reproduce the thermodynamic properties of a range of molecules has also been examined[4]. Specifically, the topologies generated by the ATB have been used to estimate the free energy of hydration of 214 diverse molecules:

  • 75 small organic molecules containing one biologically relevant functional group.
  • 92 chemically diverse drug (or drug-like) molecules taken from the Statistical Assessment of the Modelling of Proteins and Ligands (SAMPL) challenges (SAMPL0, SAMPL1, SAMPL2)[5-7].
  • 47 drug-like molecules from the recent SAMPL4 challenge.

The free energies of hydration were calculated using thermodynamic integration as implemented in the GROMOS11[3] package using a fully automated protocol that incorporates a dynamic analysis of the convergence and integration error in the selected intermediate points[4].

The results for all 214 molecules are presented graphically in Fig. 3, which shows a plot of the values calculated using parameters generated by the ATB version 2.0 based on the GROMOS 53A6[8] united atom (UA) force field versus the experimental values. As can be seen in Fig. 3 the points lay equality distributed about a line corresponding to a one-to-one agreement between the calculated and experimental values. For the UA topologies the average error (AE) was 0.29 kJ/mol, the root mean square error (RMSE) was 9.49 kJ/mol, the average unsigned error (AUE) was 6.71 kJ/mol, the Kendall tau statistic (Tau) was 0.75, the Pearson correlation coefficient (R) was 0.91 and the slope of a line of best fit using linear regression was 1.12. The statistics for the SAMPL4 molecules were similar to that obtained for the whole data set.


Fig. 3. Hydration free energies for a test set of 214 molecules calculated using parameters generated by the ATB 2.0. The 167 molecules, which had been used to test previous version of the ATB, are shown as blue crosses while the SAMPL4 molecules are indicated by yellow triangles. The solid line has a slope of one and represents a one-to-one agreement between the calculated and experimental numbers. The two dotted lines represent a 5 kJ/mol deviation from the ideal line.



A subset of 75 small organic molecules consisting of alcohols, alkanes, cycloalkanes, alkenes, alkynes, alkyl benzenes, amines, amides, aldehydes, carboxylic acids, esters, ketones, thiols and sulphides was used as an initial test of the ATB parameters. The AUE for these molecules was 3.37 kJ/mol and 77% of the molecules lay within 5 kJ/mol of the experimental value. The largest deviation from experiment was 8.5 kJ/mol. What is clear from this result is that while the ATB parameters perform well for the majority of molecules, certain functional groups lead to systematic deviations from experiment (Fig. 4).


Fig. 4. Hydration free energies for 75 small organic molecules calculated using parameters generated by the ATB 2.0. The solid line has a slope of one and represents a one-to-one agreement between the calculated and experimental numbers. The two dotted lines represent a 5 kJ/mol deviation from the ideal line.



Of the set of 167 molecules, 92 were taken from previous SAMPL challenges. The AUE for molecules in the SAMPL0, SAMPL1 and SAMPL2 data sets were 7.2 kJ/mol, 9.6 kJ/mol and 8.5 kJ/mol respectively. While approximately 40% still lay within 5 kJ/mol of the experimental value the largest deviation from experiment was 42 kJ/mol. This is in part a reflection of the uncertainty in the experimental hydration free energies of molecules contained in SAMPL challenges (which were as large as 8 kJ/mol) and in part a reflection of the fact that these molecules contained a range of functional groups not commonly found in biomolecular systems.


Summary

The ATB 2.0 parameters were validated against structural data such as root mean square deviation and thermodynamic data such as hydration free energies:

  • Structural validation has shown good overall agreement between the QM optimized structures and the energy minimized structures using the ATB parameters.
  • The agreement between the predicted and experimental hydration free energies for the majority of molecules investigated is good.
  • The average unsigned-error (AUE) using ATB 2.0 topologies for the complete test set is 6-7 kJ/mol. However, for molecules containing functional groups that form part of the main GROMOS force field[8] the AUE is 3-4 kJ/mol.
  • The systematic nature of the deviations suggests that it will be possible to greatly improve the overall performance of the ATB by optimizing the parameters for a small number of non-optimal atom types.


    1. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. J Comput Chem 14 (11):1347-1363.
    2. Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular Forces. Springer Netherlands, The Netherlands, pp 331-342. doi:10.1007/978-94-015-7658-1_21
    3. Schmid N, Christ CD, Christen M, Eichenberger AP, van Gunsteren WF (2012) Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. Comput Phys Commun 183 (4):890-903.
    4. Koziara KB, Stroet M, Malde AK, Mark AE (2013) Testing and validation of the Automated Topology Builder (ATB) version 2.0: Prediction of hydration freee enthalpies. J Comput Aided Mol Des [in press].
    5. Geballe MT, Skillman AG, Nicholls A, Guthrie JP, Taylor PJ (2010) The SAMPL2 blind prediction challenge: introduction and overview. J Comput Aided Mol Des 24 (4):259-279.
    6. Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS (2008) Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. J Med Chem 51 (4):769-779.
    7. Guthrie JP (2009) A blind challenge for computational solvation free energies: introduction and overview. J Phys Chem B 113 (14):4501-4507.
    8. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 25 (13):1656-1676.

About ATB

Overview

The ATB and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include:

  • The study of biomolecule:ligand complexes
  • Free energy calculations
  • Structure-based drug design
  • The refinement of x-ray crystal complexes

This site provides:

  • A repository for building blocks and interaction parameter files for molecules described using GROMOS force fields.
  • An automated builder to help generate building blocks for novel molecules, compatible with the GROMOS 53A6 force field and in formats appropriate for the GROMACS, GROMOS simulation packages and CNS, Phenix, CCP4 and Refmac5 X-ray refinement packages.
  • Refined geometries for molecules within the repository.
  • Equilibrated starting coordinates for a range of biologically important systems.

Required Input:

  • A coordinate file in Protein Data Bank (PDB) format (including all hydrogen atoms).
  • A connectivity record in PDB format listing all interatomic bonds.
  • The net charge on the molecule.

Output Provided:

  • Building block files (all atom and united atom).
  • Interaction parameter files for the corresponding force field.
  • Optimized geometries (all atom and united atom).

The building block and interaction parameter files are provided in a range of formats that can be used to generate the appropriate topology files.

The ATB Pipeline

The topology builder uses a knowledge-based approach in combination with QM calculations to select parameters consistent with a given force field.

The molecule is initially optimised at the HF/STO-3G (or AM1 or PM3) level then re-optimised at the B3LYP/6-31G* level of theory in implicit solvent (water). The initial charges are estimated by fitting the electrostatic potential using Kollmann-Singh scheme. The Hessian matrix is calculated.

The topology is constructed as follows:

  1. A template building block is generated based on the connectivity records including all possible bonds, angles and dihedral angles.
  2. Atom types and mass types are assigned based on the original PDB file.
  3. An initial list of 1-2 and 1-3 exclusions is generated based on connectivity.
  4. Initial charges are assigned based on QM charges or similarity to known groups.
  5. Charge groups are assigned based on atom connectivity and initial partial charges.
  6. Atoms are reordered based on charge groups.
  7. Bond and angle types are assigned based on (1) atom types, (2) bond lengths or bond angles in the QM optimised geometry and (3) matching force constants derived from the Hessian matrix. Multiple options are listed in ambiguous cases and new types introduced if required.
  8. Redundant proper dihedrals are removed. The multiplicity is determined based on connectivity and substituents. The phase shift is determined by requiring that the optimised lie close to a minimum in the dihedral potential. The force constant is selected based on a combination of atom type and the difference between the QM and classical Hessians. In ambiguous cases multiple options are presented.
  9. Aromatic rings and planar groups are identified based on atom type, connectivity and the optimised geometry.
  10. Improper dihedrals are assigned.
  11. Additional 1-4 exclusions are introduced into aromatic systems.
  12. The charges on atoms in equivalent chemical environments connected by 1, 2, 3, and 4 bonds are averaged.
  13. Any symmetry within the molecules is detected and the charges averaged.
  14. Charge scaling is applied to ensure charges are compatible with the chosen parameter set.
  15. A united atom topology building block is generated from the all atom topology building block by (1) collapsing the charges on the non-polar hydrogen atoms onto the heavy atoms to which they are attached, (2) introducing improper dihedrals to maintain chirality, (3) regenerating exclusion lists and (4) reassigning atoms types as required.
  16. The final files are then converted into a range of formats and the original coordinate files reordered to match that of the building blocks.

Release Notes
Version 2.1 (Sep 14)
Version 2.1 (Aug 14)
Version 2.0 (Sep 13)
Version 2.0 (Jun 14)
Version 1.2 (Dec 12)
Version 1.1 (Aug 12)
Version 1.0 (Oct 11)

Acknowledgements

We would like to acknowledge the many people who have provided feedback during the development phase of this project, in particular, Wilfred van Gunsteren, Philippe Hünenberger, Volker Knecht, Alexandre Bonvin, Bruno Horta, Samuel Genheden and MD group at The University of Queensland, Australia

We would also like to thank Peter Ertl for providing us with the JSME molecular builder.

Useful Links

Software and tools:

  • GROMOS home page.
  • GROMACS home page.
  • Vienna-PTM a resource for generating protein post-translational modification structures for use in molecular dynamics simulations.
  • PDBeChem a dictionary of chemical components referred to in PDB entries.
  • Phenix a software suite for the automated determination of macromolecular structures using X-ray crystallography.
  • CCP4 an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography.

Conferences:

Related Literature

ATB papers:

  • 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(12), 4026-4037.
    DOI: 10.1021/ct200196m

  • Canzar S, El-Kebir M, Pool R, Elbassioni K, Malde AK, Mark AE, Geerke DP, Stougie L, Klau GW.
    Charge Group Partitioning in Biomolecular Simulation.
    Journal of Computational Biology, 2013, 20, 188-198.
    DOI:10.1089/cmb.2012.0239

  • Koziara KB, Stroet M, Malde AK, Mark AE.
    Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
    Journal of Computer-Aided Molecular Design, 2014.
    DOI:10.1007/s10822-014-9713-7

GROMOS papers:

  • Schmid N, Christ CD, Christen M, Eichenberger AP and van Gunsteren WF.
    Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation.
    Computer Physics Communications, 2012, 183, 890-903.
    DOI:10.1016/j.cpc.2011.12.014

  • Eichenberger AP, Allision JR, Dolenc J, Geerke DP, Horta BAC, Meier K, Oostenbrink C, Schmid N, Steiner D, Wang DQ and van Gunsteren WF.
    GROMOS plus plus Software for the Analysis of Biomolecular Simulation Trajectories.
    Journal of Chemical Theory and Computation, 2011, 7, 3379-3390.
    DOI:10.1021/ct2003622

GROMOS 54A7:

  • Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE and van Gunsteren WF.
    Definition and testing of the GROMOS force-field versions 54A7 and 54B7.
    European Biophysics Journal, 2011, 40, 843-856.
    DOI: 10.1007/s00249-011-0700-9

GROMOS 53A6:

  • Oostenbrink C, Villa A, Mark AE and van Gunsteren WF.
    A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6.
    Journal of Computational Chemistry, 2004, 25, 1656-1676.
    DOI: 10.1002/jcc.20090

GROMOS Lipid Forcefields:

  • Poger D, Mark AE and van Gunsteren WF.
    A new force field for simulating phosphatidylcholine bilayers.
    Journal of Computational Chemistry, 2010, 31, 1117-1125.
    DOI: 10.1002/jcc.21396

  • Poger D and Mark AE.
    On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment.
    Journal of Chemical Theory and Computation, 2010, 6, 325-336.
    DOI: 10.1021/ct900487a

GROMOS Sugar Forcefields:

  • Lins RD and Hünenberger PH.
    A new GROMOS force field for Hexopyranose-based carbohydrates.
    Journal of Computational Chemistry, 2005, 26, 1400-1412.
    DOI:10.1002/jcc.20275

  • Hansen HS and Hünenberger PH. A Reoptimized GROMOS Force Field for Hexopyranose-Based Carbohydrates Accounting for the Relative Free Energies of Ring Conformers, Anomers, Epimers, Hydroxymethyl Rotamers, and Glycosidic Linkage Conformers.
    Journal of Computational Chemistry, 2011, 32, 998-1032.
    DOI:10.1002/jcc.21675

Collaborators

FAQ

Frequently Asked Questions (FAQ)

How can I find an existing molecule on the ATB?

Under the "Existing Molecules" tab on the ATB there is a search utility under "Match" a field. One can search for a molecule using a molecular formula, IUPAC name, common name or Canonical SMILES. The easiest way to search is using a molecular formula as the primary search criteria and select the appropriate molecule from either IUPAC name and/or Canonical SMILES.

Can I submit a ligand (heteromolecule) molecule as is from a PDB file?

No. The ligand molecules in most PDB files only contain HEAVY ATOMS. The complete ligand molecule (with all HYDROGEN atoms and correct tautomeric and protonation states as well as its formal charge) must be submitted to the ATB. Only then isit possible for the ATB to generate a complete topology file. A range of programs such as ArgusLab or Avogadro can be used to edit the hydrogen atoms in a ligand molecule.

The ATB only generates a complete topology for molecules containing <40 atoms. How can I generate a reliable topology for a larger molecule?

Although the ATB only generates a complete topology for molecules containing <40 atoms, it can be used to create an initial template for a larger ligand molecule. This template contains all atom-type information and bonded parameters. In some cases, initial estimates of the charges may also be given. Before use, these templates need to be examined and where necessary edited manually. In order to obtain more precise parameters, a larger molecule can be broken into smaller fragments and the parameters from these fragments can be used to complete the template of the larger molecule.

How do I use the JSME builder?

1. For those of you who don't know much about JSME and JSMol, JSME on the left hand side is 2D molecule builder and JSMol on the right hand side is a molecule viewer in 3D.

2. The function of buttons on JSME molecule builder is straightforward, but it is still worth mentioning that the "white rectangular" shaped button is used to wipe out the molecule to rebuild from the start."+/-" labeled button can add and move hydrogen atoms to create ions. The the pike-shaped button works as chirality specifier. For more information about how to use JSME, please find in manual.

3. To submit a molecule, you need to click on the pink button to feed and visualize the structure in Jmol before clicking submit to generate the structure in PDB format and close the popup window.

How can I generate a topology for a peptide/protein or polysaccharide?

The ATB is designed to generate the force field topology for a ligand molecule (up to ~100 atoms). To generate larger polymeric molecules such as proteins or polysacharides there are specific tools (make_top in GROMOS and pdb2gmx in GROMACS) available to combine building block files containing individual amino acids or sugars to generate the complete topologies for a larger molecule. These building blocks are highly optimized and should be used in preference to the topologies generated directly by the ATB.

Can I submit a ligand molecule containing a metal atoms such as metal:ligand complexes?

At present, the ATB has a limited capacity to handle metal ions. Currently, the GROMOS force field does not include paramaters for transition metals other than for Cu+, Cu2+, Zn2+ and Fe2+. If a molecule is submitted that contains other metal ions, the ATB will terminate after the generation of the initial template topology. To generate a complete topology file for a metal:ligand complex, each ligand should be submitted separately to the ATB. The parameters for the individual ligands can then be transferred to the template of the complete complete complex. The charges on the metal ion and any changes to the ligand topology would need to be added manually. We recommended to use ab initio quantum mechanical or density functional theory methods to study metal ion coordination in detail.

How do I cite the Automated Topology Builder (ATB) and Repository?

The following paper describes the ATB and its validation:

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(12), 4026-4037. DOI: 10.1021/ct200196m

For ATB version 2.0 topologies please also site:

Canzar S, El-Kebir M, Pool R, Elbassioni K, Malde AK, Mark AE, Geerke DP, Stougie L, Klau GW. Charge Group Partitioning in Biomolecular Simulation. Journal of Computational Biology, 2013, 20, 188-198. DOI:10.1089/cmb.2012.0239

Koziara KB, Stroet M, Malde AK, Mark AE. Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. Journal of Computer-Aided Molecular Design, 2014. DOI: 10.1007/s10822-014-9713-7

The following papers describe the various versions of the GROMOS force field used in the ATB.

  1. Oostenbrink C, Villa A, Mark AE and van Gunsteren WF. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 2004, 25, 1656-1676. DOI: 10.1002/jcc.20090
  2. Poger D, Mark AE and van Gunsteren WF. A new force field for simulating phosphatidylcholine bilayers Journal of Computational Chemistry, 2010, 31, 1117-1125. DOI: 10.1002/jcc.21396
  3. Poger D and Mark AE. On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment. Journal of Chemical Theory and Computation, 2010, 6, 325-336. DOI: 10.1021/ct900487a
  4. Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE and van Gunsteren WF. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal, 2011, 40, 843-856. DOI: 10.1007/s00249-011-0700-9