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Recent changes:

  • 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.
  • The ATBs molecular drawer has been changed to JSME in order to avoid browser security issues.
  • The ATBs IFP file (in GROMOS++ format) is now compatible with the latest GROMOS release.

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.

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 1 204 143
amino acid building block 60 205 0
heteromolecule 61 13 10249
lipid 56 6 202
nucleic acid 0 1 22
solvent 8 0 46
sugar 14 0 185
sugar building block 3 0 0

Total molecules: 11479
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 (12458)
Page: of 125
Display:
Molecule ID Formula IUPAC Name Common Name/Description Atoms Charge Forcefield Submission Date FilesCuration
20597 C19H23N7O6 (2S)-2-{[4-({[(8aS)-2-amino-4- ... dhf 53 -2 multiple 2014-08-28 Link ATB
20596 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... L80C0 80 0 multiple 2014-08-27 Link ATB
20595 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... L80C1 80 0 multiple 2014-08-27 Link ATB
20589 C56H114O28 2,5,8,11,14,17,20,23,26,29,32, ... peo 27 198 0 multiple 2014-08-27 Link ATB
20588 C38H78O19 2,5,8,11,14,17,20,23,26,29,32, ... peo 18 135 0 multiple 2014-08-27 Link ATB
20587 C20H42O10 2,5,8,11,14,17,20,23,26,29-dec ... PEO 9 72 0 multiple 2014-08-27 Link ATB
20586 C16H22N2O5 {[(2R)-2-{[(S)-(butylcarbamoyl ... ehmi001_cooh 45 0 multiple 2014-08-27 Link Partial
20584 C10H18O (2E)-3,7-dimethylocta-2,6-dien ... ger 29 0 multiple 2014-08-27 Link ATB
20580 C18H38O10 3,6,9,12,15,18,21,24-octaoxahe ... peg Mw 400 66 0 multiple 2014-08-27 Link ATB
20578 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... UchL80C2 80 0 multiple 2014-08-26 Link ATB
20576 C21H33N5O2 3-butyl-1-[(4-{[(4R)-2-imino-4 ... L61C4 61 0 multiple 2014-08-26 Link ATB
20575 C21H33N5O2 3-butyl-1-[(4-{[(4R)-2-imino-4 ... L61C3 61 0 multiple 2014-08-26 Link ATB
20574 C21H33N5O2 3-butyl-1-[(4-{[(4R)-2-imino-4 ... L61C2 61 0 multiple 2014-08-26 Link ATB
20573 C21H33N5O2 3-butyl-1-[(4-{[(4R)-2-imino-4 ... L61C1 61 0 multiple 2014-08-26 Link ATB
20572 C21H33N5O2 3-butyl-1-[(4-{[(4R)-2-imino-4 ... L61C0 61 0 multiple 2014-08-26 Link ATB
20571 C9H10O2 benzyl acetate benzyl acetate 21 0 multiple 2014-08-26 Link ATB
20567 C9H10O2 benzyl acetate benzyl ester 21 0 multiple 2014-08-26 Link ATB
20566 C8H18O5 2-{2-[2-(2-hydroxyethoxy)ethox ... PEG Mw 200 31 0 multiple 2014-08-26 Link ATB
20565 C9H14N 1-butylpyridine N-n-Butylpyridinium 24 1 multiple 2014-08-26 Link ATB
20561 C8H16 ethylcyclohexane CHA 24 0 multiple 2014-08-26 Link ATB
20558 C6H13O9P dihydroxy(oxo){[(2R,3S,4S,5R,6 ... 5yh 27 -2 multiple 2014-08-26 Link ATB
20557 C16H18N3S 3-N,3-N,7-N,7-N-tetramethyl-5 ... Methylene blue no Cl 38 1 multiple 2014-08-26 Link ATB
20553 C16H18N3S 3-N,3-N,7-N,7-N-tetramethyl-5 ... Methylene blue 38 1 multiple 2014-08-25 Link ATB
20551 C60H82O60 Alginate-10M_np 192 -10 multiple 2014-08-25 Link ATB
20550 C30H42O31 Alginate-5M 98 -5 multiple 2014-08-25 Link ATB
20549 C60H82O61 Alginate-10G_np 193 -10 multiple 2014-08-25 Link ATB
20546 C30H42O31 Alginate-5G 98 -5 multiple 2014-08-25 Link ATB
20545 C20H25ClN6O3 2-chloro-4-[(2-{[(2R)-1-hydrox ... L49C4 55 0 multiple 2014-08-25 Link ATB
20542 C21H36N5O2 (2R)-N-[(4-{[(butylcarbamoyl)a ... L61C2 63 0 multiple 2014-08-25 Link ATB
20541 C21H36N5O2 (2R)-N-[(4-{[(butylcarbamoyl)a ... L61C1 63 0 multiple 2014-08-25 Link ATB
20540 C21H36N5O2 (2R)-N-[(4-{[(butylcarbamoyl)a ... L61C0 63 0 multiple 2014-08-25 Link ATB
20539 C36H50O37 Alginate-6G 117 -6 multiple 2014-08-25 Link ATB
20538 C35H39Cl2N3O3 (1R,5S)-N-cyclopropyl-7-{4-[2- ... L40C4 82 0 multiple 2014-08-25 Link ATB
20537 C35H39Cl2N3O3 (1R,5S)-N-cyclopropyl-7-{4-[2- ... L40C3 82 0 multiple 2014-08-25 Link ATB
20536 C35H39Cl2N3O3 (1S,5R)-N-cyclopropyl-7-{4-[2- ... L40C2 82 0 multiple 2014-08-25 Link ATB
20535 C35H39Cl2N3O3 (1R,5S)-N-cyclopropyl-7-{4-[2- ... L40C1 82 0 multiple 2014-08-25 Link ATB
20534 C35H39Cl2N3O3 (1S,5R)-N-cyclopropyl-7-{4-[2- ... L40C0 82 0 multiple 2014-08-25 Link ATB
20533 C26H29NO2 4-[(1Z)-1-{4-[2-(dimethylamino ... L69C3 58 0 multiple 2014-08-25 Link ATB
20532 CH4S2 methanedithiol CS2 3 0 multiple 2014-08-25 Link ATB
20531 C16H36P tetrabutyl-λ5-phosphane Tetrabutylphosphonium ion 53 1 multiple 2014-08-24 Link ATB
20525 C41H83NO8P (2R)-1-{[(R)-(2-aminoethoxy)(h ... DSPE 133 0 multiple 2014-08-23 Link ATB
20524 C7H9N2O (E)-N-[(1-methylpyridin-2-yl)m ... 2-PAM zwitterion 18 0 multiple 2014-08-23 Link ATB
20523 C7H9N2O (E)-N-[(1-methylpyridin-2-yl)m ... 2-PAM test zwitterion 18 0 multiple 2014-08-23 Link ATB
20522 C7H9N2O (E)-N-[(1-methylpyridin-2-yl)m ... 2-PAM test 19 1 multiple 2014-08-23 Link ATB
20521 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... L53C4 52 0 multiple 2014-08-23 Link ATB
20520 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... L53C3 52 0 multiple 2014-08-23 Link ATB
20519 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... L53C2 52 0 multiple 2014-08-23 Link ATB
20518 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... L53C1 52 0 multiple 2014-08-23 Link ATB
20517 C7H9N2O (E)-N-[(1-methylpyridin-2-yl)m ... 2-PAM (Hydrogens) 19 1 multiple 2014-08-23 Link ATB
20516 C29H33NO4 1-{2-[(2S)-2-hydroxy-3-(4-hydr ... 62 67 0 multiple 2014-08-23 Link ATB
20515 C5H12O7P2 dihydroxy({[(R)-hydroxy(λ3 ... IPPv2 23 -3 multiple 2014-08-23 Link Partial
20513 C7H9N2O (E)-N-[(1-methylpyridin-2-yl)m ... 2-PAM (correct) 19 1 multiple 2014-08-23 Link ATB
20510 C18H26O19 Alginate-3M_np 60 -3 multiple 2014-08-22 Link ATB
20509 C18H26O19 Alginate-3G_np 60 -3 multiple 2014-08-22 Link ATB
20507 C50H70O49 Alginate-M_test 161 -8 multiple 2014-08-22 Link ATB
20506 C8H15N2 1-butyl-3-methylimidazole 25 1 multiple 2014-08-22 Link ATB
20505 C7H9N2O (E)-N-[(1-methylpyridin-2-yl)m ... 2-PAM 19 1 multiple 2014-08-22 Link ATB
20501 C21H30N3O (4-{4-[(E)-2-(4-ethylphenyl)di ... trans 55 1 multiple 2014-08-22 Link ATB
20500 C21H30N3O (4-{4-[(E)-2-(4-ethylphenyl)di ... Cis 55 1 multiple 2014-08-22 Link ATB
20498 C40H82O20 2,5,8,11,14,17,20,23,26,29,32, ... PEO 18 142 0 multiple 2014-08-22 Link ATB
20497 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... UchL80C4 80 0 multiple 2014-08-22 Link ATB
20496 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... UchL80C3 80 0 multiple 2014-08-22 Link ATB
20495 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... UchL80C2 80 0 multiple 2014-08-22 Link ATB
20494 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... UchL80C1 80 0 multiple 2014-08-22 Link ATB
20493 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... UchL80C1 80 0 multiple 2014-08-22 Link ATB
20492 C34H34F2N4O6 1-N'-[3-fluoro-4-({6-methoxy-7 ... UchL80C0 80 0 multiple 2014-08-22 Link ATB
20491 C26H29NO2 4-[(1Z)-1-{4-[2-(dimethylamino ... UchL69C4 58 0 multiple 2014-08-22 Link ATB
20490 C21H23F2N5O2 4-N-(2,6-difluorophenyl)-6-N-{ ... UchL69C3 53 0 multiple 2014-08-22 Link ATB
20489 C26H29NO2 4-[(1Z)-1-{4-[2-(dimethylamino ... UchL69C2 58 0 multiple 2014-08-22 Link ATB
20488 C26H29NO2 4-[(1Z)-1-{4-[2-(dimethylamino ... UchL69C1 58 0 multiple 2014-08-22 Link ATB
20487 C26H29NO2 4-[(1Z)-1-{4-[2-(dimethylamino ... UchL69C0 58 0 multiple 2014-08-22 Link ATB
20486 C21H23F2N5O2 4-N-(2,6-difluorophenyl)-6-N-{ ... UchL63C4 53 0 multiple 2014-08-22 Link ATB
20485 C21H23F2N5O2 4-N-(2,6-difluorophenyl)-6-N-{ ... UchL63C3 53 0 multiple 2014-08-22 Link ATB
20484 C21H23F2N5O2 4-N-(2,6-difluorophenyl)-6-N-{ ... UchL63C2 53 0 multiple 2014-08-22 Link ATB
20483 C21H23F2N5O2 4-N-(2,6-difluorophenyl)-6-N-{ ... UchL63C1 53 0 multiple 2014-08-22 Link ATB
20482 C21H23F2N5O2 4-N-(2,6-difluorophenyl)-6-N-{ ... UchL63C0 53 0 multiple 2014-08-22 Link ATB
20481 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... UchL53C4 52 0 multiple 2014-08-22 Link ATB
20480 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... UchL53C3 52 0 multiple 2014-08-22 Link ATB
20479 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... UchL53C2 52 0 multiple 2014-08-22 Link Partial
20478 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... UchL53C2 52 0 multiple 2014-08-22 Link Partial
20477 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... UchL53C1 52 0 multiple 2014-08-22 Link Partial
20476 C19H25N5O3 9-butyl-8-[(3,4,5-trimethoxyph ... UchL53C0 52 0 multiple 2014-08-22 Link ATB
20474 C20H25ClN6O3 2-chloro-4-[(2-{[(2S)-1-hydrox ... UchL49C3 55 0 multiple 2014-08-21 Link ATB
20473 C20H25ClN6O3 2-chloro-4-[(2-{[(2R)-1-hydrox ... UchL49C2 55 0 multiple 2014-08-21 Link ATB
20472 C20H25ClN6O3 2-chloro-4-[(2-{[(2R)-1-hydrox ... UchL49C1 55 0 multiple 2014-08-21 Link ATB
20471 C20H25ClN6O3 2-chloro-4-[(2-{[(2R)-1-hydrox ... UchL49C0 55 0 multiple 2014-08-21 Link ATB
20470 C27H25N4O6 UchL43C4 59 0 multiple 2014-08-21 Link ATB
20469 C27H25N4O6 UchL43C3 59 0 multiple 2014-08-21 Link ATB
20468 C27H25N4O6 UchL43C2 59 0 multiple 2014-08-21 Link ATB
20467 C27H25N4O6 UchL43C1 59 0 multiple 2014-08-21 Link ATB
20466 C27H25N4O6 UchL43C0 59 0 multiple 2014-08-21 Link ATB
20465 C35H39Cl2N3O3 (1R,5S)-N-cyclopropyl-7-{4-[2- ... UchL40C4 82 0 multiple 2014-08-21 Link ATB
20464 C35H39Cl2N3O3 (1R,5S)-N-cyclopropyl-7-{4-[2- ... UchL40C3 82 0 multiple 2014-08-21 Link ATB
20463 C35H39Cl2N3O3 (1S,5R)-N-cyclopropyl-7-{4-[2- ... UchL40C2 82 0 multiple 2014-08-21 Link ATB
20462 C35H39Cl2N3O3 (1R,5S)-N-cyclopropyl-7-{4-[2- ... UchL40C1 82 0 multiple 2014-08-21 Link ATB
20461 C35H39Cl2N3O3 (1S,5R)-N-cyclopropyl-7-{4-[2- ... UchL40C0 82 0 multiple 2014-08-21 Link ATB
20460 C8H15N2 1-butyl-3-methylimidazole 25 1 multiple 2014-08-21 Link ATB
20459 C20H21NO6S (2R)-6-methoxy-2-{[4-(4-methox ... UchL23C4 49 0 multiple 2014-08-21 Link ATB
20458 C20H21NO6S (2R)-6-methoxy-2-{[4-(4-methox ... UchL23C3 49 0 multiple 2014-08-21 Link ATB
20457 C20H21NO6S (2R)-6-methoxy-2-{[4-(4-methox ... UchL23C2 49 0 multiple 2014-08-21 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

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 2.0 (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 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

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.

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 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.

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.

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.