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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.

News

Recent changes:

  • The ATB has been recently updated, 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 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:

Conditions of Use

The Automated Topology Builder (ATB) and Repository has been developed and is currently maintained with support from the University of Queensland (UQ), the Australian Research Council (ARC) and the Queensland Cyber Infrastructure Foundation (QCIF). Access to the ATB is provided free to academic users from publically funded teaching or research institutions. Access for academic use is conditional on: i) any molecule submitted to the ATB being made publically available and ii) the source of any material downloaded from the ATB being properly acknowledged in any publications or other forms in which research using this material is disseminated.

Use of the ATB by other parties, or academic users wishing to restrict the access of others to specific molecules, is considered to be commercial in nature. Commercial access is available by licence or collaborative agreement. Parties interested in commercial licencing or other arrangements should contact Prof Alan E. Mark at the address provided at the bottom of the page.

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 registered to use the ATB but have either forgotten or have not received your password, please go here to generate a new 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 1 204 239
amino acid building block 60 205 0
heteromolecule 61 13 12443
lipid 56 6 278
nucleic acid 0 1 26
solvent 8 0 81
sugar 14 0 226
sugar building block 3 0 0

Total molecules: 13925
Search
Search string*:
Molecule type:
Curation:
* The search string is matched to IUPAC Name,
  Common Name, Residue Name,
  Formula and Canonical SMILES
Selected Molecules (14295)
Page: of 143
Display:
Molecule ID Formula IUPAC Name Common Name Atoms Charge Forcefield Submission Date Files Curation
24661 C8H13N2O5 28 -1 multiple 2015-04-26 Link Partial
24660 C10H13NO2 N-[2-(methoxymethyl)phenyl]ace ... 26 multiple 2015-04-26 Link Partial
24659 C25H22N4O12S4 [2-({4-[(4-{[4-(methylamino)-3 ... 67 multiple 2015-04-26 Link ATB
24658 C12H15N2O2 4-(2-aminoethyl)-7-(methylamin ... 31 1 multiple 2015-04-26 Link ATB
24657 C128H242N16O81 467 multiple 2015-04-26 Link Partial
24656 C27H36F2O6 2-[(1R,2S,8S,10S,11S,13R,14R,1 ... Losalen 71 multiple 2015-04-26 Link Partial
24655 disodium 2 2 multiple 2015-04-26 Link ATB
24653 C7H12N2O4 1,3-bis(hydroxymethyl)-5,5-dim ... DMDMhydantoin 25 multiple 2015-04-26 Link ATB
24647 C10 (1S,7R)-8,8-dimethyltetracyclo ... 10 multiple 2015-04-25 Link ATB
24644 C7H6O2 2-formylbenzen-1-olate Salicylaldehyde 15 multiple 2015-04-25 Link Partial
24643 C10O 6,6-dimethyl-7-oxatricyclo[3.2 ... 11 multiple 2015-04-25 Link ATB
24642 C15H5N4O2 [(6-{2-[3-(buta-1,3-diyn-1-yl) ... 26 1 multiple 2015-04-25 Link Partial
24640 C26H24N4O6S2 [5-(methylamino)-2-{[4-({4-[(4 ... 62 multiple 2015-04-25 Link ATB
24639 C36H26O2 7,16-bis(4-ethylphenyl)-12,22- ... 64 multiple 2015-04-25 Link ATB
24637 C40H80NO8P (2R)-1-(decanoyloxy)-3-{[(2S)- ... (2R)-3-(Decanoyloxy)-2-(docosa ... 130 multiple 2015-04-25 Link ATB
24635 C70H132O17P2 (2R)-1-{[(2R,5S)-7-[(S)-[(2R)- ... 221 multiple 2015-04-25 Link Partial
24634 C57H60O21S7 dihydroxy({4-[(2S,4R,6S,8r,10R ... 138 -7 multiple 2015-04-24 Link Partial
24630 C14H22O4 1-(3-methylphenyl)-1,4,7,10-te ... 40 multiple 2015-04-24 Link ATB
24629 C15H14O4 5-[(E)-2-(3-methoxy-4-oxidophe ... Isorhapontigenin 33 multiple 2015-04-24 Link ATB
24628 C7H8N2 benzenecarboximidamide 17 multiple 2015-04-24 Link ATB
24627 C24H46O6 (2R)-2-[(2R,3S,4R)-3,4-dihydro ... 76 multiple 2015-04-24 Link ATB
24626 C24H46O6 (2R)-2-[(2R,3S,4R)-3,4-dihydro ... 76 multiple 2015-04-24 Link ATB
24625 C128H211N5O13 1,5-bis({11-[(1R,2R,3s,4r,5R,9 ... 357 multiple 2015-04-23 Link ATB
24624 C10H16N5O13P3 ({[({[(2R,3S,4R,5R)-5-(6-amino ... 47 multiple 2015-04-23 Link ATB
24623 C21H26N2O4 8-[(1R)-1-hydroxy-2-{[2-methyl ... 5-Hydroxy-8-[(1R)-1-hydroxy-2- ... 53 multiple 2015-04-23 Link ATB
24622 C20H41N (2R,6R)-2-methyl-6-tetradecylp ... 62 multiple 2015-04-23 Link ATB
24621 C5H10O5 (2R,3R,4S)-2,3,4,5-tetrahydrox ... L-(+)-Lyxose 20 multiple 2015-04-23 Link ATB
24619 C6H12O6 (2R,3S,4R,5R)-2,5-bis(hydroxym ... beta-D-Tagatofuranose 24 multiple 2015-04-23 Link ATB
24618 C32H24N2O3 N-(4-{4-[(1R,15S,19R)-16,18-di ... 61 multiple 2015-04-23 Link ATB
24615 C5H10O2 2-methylbut-3-ene-2-peroxol 2-Methyl-3-buten-2-ylhydropero ... 17 multiple 2015-04-23 Link ATB
24614 C9O (6R)-6-(prop-1-yn-1-yl)cyclohe ... 10 multiple 2015-04-22 Link ATB
24611 C27H46O2 (1S,2R,5S,9R,10S,11S,14R,15R)- ... 5-Cholestene-3beta,7beta-diol 75 multiple 2015-04-22 Link ATB
24610 C21H40O4 (2S)-2,3-dihydroxypropyl (9E)- ... (2S)-2,3-Dihydroxypropyl(9E)-9 ... 65 multiple 2015-04-22 Link ATB
24609 C21H42O4 (2S)-2,3-dihydroxypropyl octad ... (2S)-2,3-Dihydroxypropylsteara ... 67 multiple 2015-04-22 Link ATB
24608 C4H8O oxolane Oxolane 13 multiple 2015-04-22 Link ATB
24605 C4H12P tetramethyl-λ5-phosphane 17 1 multiple 2015-04-22 Link ATB
24604 C23H26P pentyltriphenyl-λ5-phospha ... 50 1 multiple 2015-04-22 Link ATB
24603 C22H24P butyltriphenyl-λ5-phosphan ... 47 1 multiple 2015-04-22 Link ATB
24602 C21H22P triphenyl(propyl)-λ5-phosp ... 44 1 multiple 2015-04-22 Link ATB
24601 C60H87N10O30 187 -5 multiple 2015-04-22 Link ATB
24600 C4H7NO6P {[(3S)-3-amino-4-oxobutanoyl]o ... 19 -1 multiple 2015-04-22 Link ATB
24599 C26H30NO2 4-[(1Z)-1-{4-[2-(dimethylamino ... 59 1 multiple 2015-04-22 Link ATB
24597 C19H42N hexadecyltrimethylamine 1-(trimethyl-λ5-azanyl)hex ... 62 1 multiple 2015-04-22 Link ATB
24596 C8H18O4P λ3-oxidanidylidenebis(2-me ... 31 -1 multiple 2015-04-22 Link ATB
24595 C16H36N bis[(2R)-2-ethylhexyl]amine 53 1 multiple 2015-04-22 Link ATB
24593 C17H38N trimethyl(tetradecyl)amine 56 1 multiple 2015-04-21 Link ATB
24592 C6H11NO N-cyclohexylidenehydroxylamine Cyclohexanoneoxime 19 multiple 2015-04-21 Link ATB
24591 C11H8N2 3H,9H-1λ4,3-naphtho[2,3-d] ... 21 multiple 2015-04-21 Link ATB
24588 C15H12N2O 2-azatricyclo[9.4.0.03,8]pe ... Carbamazepine 30 multiple 2015-04-21 Link ATB
24586 C10H18O 2-[(1R)-4-methylcyclohex-3-en- ... (R)-(+)-alpha-Terpineol 29 multiple 2015-04-21 Link ATB
24585 F6P hexafluoro-λ5-phosphanium 7 -1 multiple 2015-04-21 Link ATB
24576 C7H8N4O2 1,3-dimethyl-1,2,3,5,6,7-hexah ... 21 multiple 2015-04-21 Link ATB
24573 C25H25N5O4 1-(4-methoxyphenyl)-7-oxo-6-[4 ... Apixaban 59 multiple 2015-04-20 Link ATB
24572 C28H37F2N3O3 N-[(2S,3R)-4-{[(4Z)-1-(3-tert- ... 73 multiple 2015-04-20 Link ATB
24570 C8H19O4P bis(2-methylpropoxy)phosphinic ... Diisobutylhydrogenphosphate 32 multiple 2015-04-20 Link ATB
24568 C23H48NO2 2-(trimethylamino)ethyl octade ... 74 1 multiple 2015-04-20 Link ATB
24567 C21H44NO2 2-(trimethylamino)ethyl hexade ... 2-(trimethyl-λ5-azanyl)eth ... 68 1 multiple 2015-04-20 Link ATB
24566 C19H40NO2 2-(trimethylamino)ethyl tetrad ... 2-(trimethyl-λ5-azanyl)eth ... 62 1 multiple 2015-04-20 Link ATB
24565 C17H36NO2 2-(trimethylamino)ethyl dodeca ... 2-(trimethyl-λ5-azanyl)eth ... 56 1 multiple 2015-04-20 Link ATB
24564 C10H12N5O10P2 {[(S)-{[(2R,3S,4R,5R)-5-(6-ami ... 39 -3 multiple 2015-04-20 Link ATB
24563 H3O3P phosphorous acid PHOSPHOROUSACID 7 multiple 2015-04-20 Link ATB
24562 C27H15N 4-azaoctacyclo[13.11.1.1 ... 43 multiple 2015-04-20 Link ATB
24561 C10H12N2O8 32 -4 multiple 2015-04-19 Link ATB
24560 C21H12O4 4-[(9,10-dioxo-9,10-dihydroant ... 37 multiple 2015-04-18 Link ATB
24559 C21H12O4 4-[(1,10-dioxo-1,10-dihydroant ... 37 multiple 2015-04-18 Link ATB
24554 C32H18N8 4,11λ4,20λ4,29λ ... 58 multiple 2015-04-18 Link ATB
24551 C5H14N3 1-butylguanidine 22 1 multiple 2015-04-18 Link ATB
24550 C19H36O10 (2R,3S,4S,5S,6S)-3,4-dimethoxy ... 65 multiple 2015-04-18 Link ATB
24549 C11H20N4O4S2.C6H12N2O2S.Zn (5R,11R)-11-acetamido-2-{[(2R) ... 62 -1 multiple 2015-04-18 Link ATB
24547 C32H18N8 4,11λ4,20λ4,29λ ... 58 multiple 2015-04-18 Link ATB
24546 C32H18N8 4,11λ4,20λ4,29λ ... 58 multiple 2015-04-18 Link ATB
24545 C19H39N (2R,6S)-2-methyl-6-tridecylpip ... 59 multiple 2015-04-18 Link ATB
24544 C30H30O8 8-formyl-2-[8-formyl-3-methyl- ... Gossypol 68 multiple 2015-04-17 Link ATB
24538 C5H13N3 1-butylguanidine 21 multiple 2015-04-17 Link ATB
24536 C8H15N3O5 (3S)-3-[(2S)-2-amino-3-hydroxy ... 31 multiple 2015-04-17 Link ATB
24534 C7H6O5 5-carboxybenzene-1,2,3-tris(ol ... Gallicacid 18 multiple 2015-04-17 Link ATB
24532 C15H30N4O3 54 multiple 2015-04-16 Link ATB
24524 C2H6O ethanol Ethanol 9 multiple 2015-04-16 Link ATB
24523 C8H18N3O2 (2E)-N-[2-(diethylamino)ethyl] ... 31 1 multiple 2015-04-16 Link ATB
24522 C8H17N3O2 (2E)-N-[2-(diethylamino)ethyl] ... 30 multiple 2015-04-16 Link ATB
24521 C10H5F17S 3,3,4,4,5,5,6,6,7,7,8,8,9,9,10 ... 3,3,4,4,5,5,6,6,7,7,8,8,9,9,10 ... 33 multiple 2015-04-16 Link ATB
24515 C34H34N4O4 76 multiple 2015-04-16 Link ATB
24510 C8H10O2 2-methoxy-4-methylbenzen-1-ola ... creosol 20 multiple 2015-04-15 Link ATB
24509 C90H148N6O66 (2R,4S,5R,6R)-2-{[(2R,3R,4S,5R ... 310 multiple 2015-04-15 Link Partial
24508 C180H254S18 3-hexyl-2-(4-hexyl-5-{4-hexyl- ... 452 multiple 2015-04-15 Link ATB
24503 C12H4Cl4O2 2,3,7,8-tetrachlorooxanthrene 2,3,7,8-Tetrachlorodibenzo-p-d ... 22 multiple 2015-04-15 Link ATB
24499 C9H9ClO4 3-chloro-4-formyl-2,6-dimethox ... 2-Chloro-4-hydroxy-3,5-dimetho ... 23 multiple 2015-04-14 Link ATB
24498 C4H7NO4 16 multiple 2015-04-14 Link ATB
24496 C16H13NO3 1-[(2-hydroxyethyl)amino]-9,10 ... 1-((2-Hydroxyethyl)amino)anthr ... 33 multiple 2015-04-14 Link ATB
24493 C11H15N5O3S (2R,3R,4S,5S)-2-(6-amino-9H-1 ... 35 multiple 2015-04-14 Link ATB
24492 C11H14N2O8P 1-[(2R,3R,4S,5R)-5-({[dihydrox ... 37 multiple 2015-04-14 Link ATB
24490 C19H24N2O2 (11bR)-2-cyclohexanecarbonyl-1 ... (R)-(-)-Praziquantel 47 multiple 2015-04-14 Link ATB
24489 C10H15NO2 (1S,2S)-2-amino-1-methoxy-3-ph ... 28 multiple 2015-04-13 Link ATB
24488 F5P pentafluoro-λ4-phosphanium Phosphoruspentafluoride 6 multiple 2015-04-13 Link ATB
24487 F2HNO4S2 [(fluorosulfonyl)amino]sulfony ... Imidodisulfuryldifluoride 10 multiple 2015-04-13 Link ATB
24486 C2HF6NO4S2 trifluoro[(trifluoromethanium) ... Bistriflimide 16 multiple 2015-04-13 Link ATB
24485 C6H11NO N-cyclohexylidenehydroxylamine Cyclohexanoneoxime 19 multiple 2015-04-13 Link ATB
24484 C6HNO N-(cyclohexa-2,5-dien-1-yliden ... 9 multiple 2015-04-13 Link ATB
24483 C6HNO N-(cyclohexa-2,5-dien-1-yliden ... 9 multiple 2015-04-13 Link ATB
24482 C7H6O2 2-formylbenzen-1-olate Salicylaldehyde 15 multiple 2015-04-13 Link ATB
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Pre-Equilibrated Systems

Pre-Equilibrated Systems in Various Phases

Name DescriptionTemperature (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

Additional GROMOS forcefield files can be found here.

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

GROMACS v-site bug fix for S-H: GROMOS54A7_for_Gromacs_3.x_4.0.x.tgz

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)

What are the conditions of use?

Access to the ATB is provided free to academic users from publically funded teaching or research institutions. Access for academic use is conditional on: i) any molecule submitted to the ATB being made publically available and ii) the source of any material downloaded from the ATB being properly acknowledged in any publications or other forms in which research using this material is disseminated. Use of the ATB by other parties, or academic users wishing to restrict the access of others to specific molecules, is considered to be commercial in nature. Commercial access is available by licence or collaborative agreement. Parties interested in commercial licencing or other arrangements should contact Prof Alan E. Mark.

Why do I need a licensing or collaborative agreement for commercial use?

The Automated Topology Builder (ATB) and Repository has been developed and is made publicly available with support from the University of Queensland (UQ), the Australian Research Council (ARC) and the Queensland Cyber Infrastructure Foundation (QCIF). The ATB also relies heavily on access to publicly funded computational resources. Specific arrangements are required for commercial use of these publicly funded facilities or if the results obtained are not made publicly available. A range of licensing and collaborative arrangements are possible and will be considered on a case-by-case basis depending on the intended use.

Are there any advantages in being a commercial user?

Commercial users (or academic users operating under a collaborative agreement) can restrict access to molecules they submit, share molecules with groups of existing users and gain access to additional functionality depending on the nature of the agreement.

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.

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

By default the ATB only generates a complete topology (based on optimization at the B3LYP/6-31G* level of theory + Hessian) for molecules containing <40 atoms when submitted by an academic user. Molecules up to 50 atoms are optimization at the B3LYP/6-31G* level of theory but no Hessian is generated. The ATB will still generate an initial template for a larger molecules (<500 atoms) based on semi-empirical methods. 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.

Why are there limits on the number of atoms?

A limit on the number of atoms for academic users is required due to the cost of processing large molecules. These limits can varied for commercial users.

The 2D sketch of the molecule appears to be incorrect.

The 2D sketch is automatically generated with OpenBabel which makes assumptions about the nature of the molecule.
To visualize the molecule as it is stored in the database select "Show Structure" from the "Select Output" table.

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.

Can I contribute to the development of the ATB?

Contributions to help further develop the functionality of the ATB either in the form of financial contributions or by assisting in the development of specific aspects of the code itself would be most welcome.

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