Home

News

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 1 204 141
amino acid building block 60 205 0
heteromolecule 61 13 10035
lipid 56 6 191
nucleic acid 0 1 22
solvent 8 0 45
sugar 14 0 175
sugar building block 3 0 0

Total molecules: 11241
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 (11989)
Page: of 120
Display:
Molecule ID Formula IUPAC Name Common Name/Description Atoms Charge Forcefield Submission Date FilesCuration
20113 C9H10NO4S.2C9H9NO4S.Fe HQS 62 -3 multiple 2014-07-30 Link Partial
20112 C32H32N6O6S2 [4-amino-3-(2-{4-[4-(2-{1-amin ... Congo Red(correct) 68 -2 multiple 2014-07-30 Link Partial
20111 C32H32N6O6S2 [4-amino-3-(2-{4-[4-(2-{1-amin ... Congo Red 68 -2 multiple 2014-07-30 Link Partial
20110 C30H54O13 (9E,17R)-17-{[(2R,3R,4S,5S,6R) ... 97 0 multiple 2014-07-30 Link ATB
20108 C18H34O3 (9E,12S)-12-hydroxyoctadec-9-e ... ricinoleic_acid 55 0 multiple 2014-07-30 Link ATB
20107 C11H19NO9 SIA 39 -1 multiple 2014-07-30 Link Partial
20105 H2O water water 3 0 multiple 2014-07-30 Link ATB
20103 C5H8O5 (2R)-2-[(2-hydroxyacetyl)oxy]p ... 1plga_test 18 0 multiple 2014-07-30 Link ATB
20102 C13H25NO8 N-[(2S,3R)-3-hydroxy-1-{[(2R,3 ... gs 47 0 multiple 2014-07-30 Link ATB
20101 C16H31NO8 N-[(2S,3R)-3-hydroxy-1-{[(2R,3 ... 56 0 multiple 2014-07-30 Link ATB
20099 C21H47O11P3.5Na (S)-((2S)-2,3-di{[bis(sodiooxy ... comp1Na 82 0 multiple 2014-07-30 Link ATB
20093 C4H6 bicyclo[1.1.0]butane toluene_cg 4 0 multiple 2014-07-29 Link ATB
20088 C23H26N5O5 2-(4-{[(2R)-2,3-dihydro-1,4-be ... doxazosin 59 1 multiple 2014-07-29 Link ATB
20087 C27H29NO11 (1S,3S)-1-{[(2R,4R,5S,6S)-4-am ... doxorubicin 68 0 multiple 2014-07-29 Link ATB
20084 C16H36N tetrabutylamine tetrabutylammonium ion 53 1 multiple 2014-07-29 Link ATB
20082 C18H20N4O6S4 3-ethyl-2-[2-(3-ethyl-6-sulfo- ... ABTS 2- 48 -2 multiple 2014-07-28 Link ATB
20080 C24H44O6 (2S)-2-[(2R,3R,4R)-3,4-dihydro ... Sorbitan Monooleate (Span 80) 74 0 multiple 2014-07-28 Link ATB
20079 C18H16O6 2-(3,4-dimethoxyphenyl)-7-meth ... Flavonaid 40 0 multiple 2014-07-28 Link ATB
20078 C15H22O11 (2S)-2-{[(2R)-2-{[(2S)-2-{[(2R ... poly-lactic3 48 0 multiple 2014-07-28 Link ATB
20077 C9H8O4 4-(acetyloxy)benzoic acid s2 21 0 multiple 2014-07-28 Link ATB
20076 C6H8O7 18 -3 multiple 2014-07-27 Link ATB
20074 C26H54 (4R,6R,8R,10S,12S,14S,16S)-2,4 ... 78 0 multiple 2014-07-26 Link ATB
20072 C7H8N4O2 3,7-dimethyl-2,3,6,7-tetrahydr ... theobromine 21 0 multiple 2014-07-26 Link ATB
20071 C200H40 cnt 240 0 multiple 2014-07-26 Link ATB
20070 C18H20N4O6S4 3-ethyl-2-[2-(3-ethyl-6-sulfo- ... ABTS 2 50 0 multiple 2014-07-26 Link ATB
20069 C18H20N4O6S4 3-ethyl-2-[2-(3-ethyl-6-sulfo- ... ABTS 50 0 multiple 2014-07-25 Link ATB
20068 C10H12O4 4-acetyl-2,6-dimethoxybenzen-1 ... Acetosyringone 26 0 multiple 2014-07-25 Link ATB
20067 C18H24N2O6 4-({2-[(3,5-dimethoxy-4-oxidop ... Syringaldazine 46 0 multiple 2014-07-25 Link ATB
20066 C17H20N2S dimethyl[3-(10H-phenothiazin-1 ... Promazine 40 0 multiple 2014-07-25 Link ATB
20065 C57H110O6 1,3-bis(octadecanoyloxy)propan ... TGL 173 0 multiple 2014-07-25 Link ATB
20057 C44H29N4O12S4.Mg tmp 89 -4 multiple 2014-07-25 Link ATB
20052 C43H79O13P (2R)-1-(hexadecanoyloxy)-3-{[( ... PI34:2 135 -1 multiple 2014-07-25 Link ATB
20050 C44H28N4O12S4.Mg 4-[(1Z,6Z,12Z,17Z)-7,12,17-tri ... Tetra-(4-sulfonatophenyl)-porp ... 89 -4 multiple 2014-07-25 Link ATB
20048 C12H16 (1S)-1-ethyl-1,2,3,4-tetrahydr ... Gre-e 28 0 multiple 2014-07-25 Link ATB
20047 C13H9N benzo[h]quinoline Gre-c 23 0 multiple 2014-07-25 Link ATB
20046 C10H10S 2-ethyl-1-benzothiophene Gre-d 21 0 multiple 2014-07-25 Link ATB
20045 C12H12 1,7-dimethylnaphthalene Gre-b 24 0 multiple 2014-07-25 Link ATB
20044 C26H56O9P2.3Na (S)-(2-[2-(2-{2-[bis(sodiooxy) ... comp2allNa 93 0 multiple 2014-07-25 Link ATB
20042 C51H40N6O23S6 8-[(4-methyl-3-{[3-({[3-({2-me ... suramin_1y4l 126 -2 multiple 2014-07-25 Link ATB
20040 C51H40N6O23S6 8-[(4-methyl-3-{[3-({[3-({2-me ... suramin_1y4l 126 0 multiple 2014-07-25 Link ATB
20034 C6H6O3S benzenesulfonic acid sideB 15 -1 multiple 2014-07-24 Link ATB
20033 C6H8N 1-methylpyridine sideA 15 1 multiple 2014-07-24 Link ATB
20020 C96H184N10O23 2-{N-[(2S)-2-ethylhexyl]-2-{N- ... 313 0 multiple 2014-07-24 Link ATB
20019 C42H79NO8P (2R)-1-(hexadecanoyloxy)-3-{[( ... PC34:3 130 0 multiple 2014-07-24 Link ATB
20018 C42H81NO8P (2R)-1-(hexadecanoyloxy)-3-{[( ... PC34:2 132 0 multiple 2014-07-24 Link ATB
20013 C39H69O8P (2R)-1-{[dihydroxy(λ3-oxid ... PA364 116 -1 multiple 2014-07-24 Link ATB
20010 C40H75O10P (2R)-3-{[(S)-[(2R)-2,3-dihydro ... PG34:2 125 -1 multiple 2014-07-24 Link ATB
20009 C38H73O10P (2R)-3-{[(S)-[(2R)-2,3-dihydro ... PG32:1 121 -1 multiple 2014-07-24 Link ATB
20008 C22H24ClFN4O3 N-(3-chloro-4-fluorophenyl)-7- ... Gefitinib 55 atoms 55 0 multiple 2014-07-24 Link ATB
20005 C4H8O oxolane tetrahydrofuran 13 0 multiple 2014-07-24 Link ATB
20002 C15H21Cl2NO5 3-[(2S,4S,5R)-5,6-dichloro-2,4 ... atpenin A5 44 0 multiple 2014-07-24 Link ATB
20001 C11H22O2 Undecanoate ion 34 -1 multiple 2014-07-24 Link ATB
20000 C16H36N tetrabutylamine Tetrabutylammonium ion 53 1 multiple 2014-07-24 Link ATB
19998 C38H73O10P (2R)-3-{[(S)-[(2R)-2,3-dihydro ... PG32:1 121 -1 multiple 2014-07-23 Link ATB
19997 C53H88O15 (2S)-1-[(9Z,12Z,15Z)-octadeca- ... DGDG36:6 156 0 multiple 2014-07-23 Link ATB
19992 C76H49N3O32 humic acid 157 -3 multiple 2014-07-23 Link ATB
19991 C8H11NO2 4-(2-aminoethyl)benzene-1,2-bi ... 22 0 multiple 2014-07-23 Link ATB
19989 H3O oxidanuide hydronium 4 1 multiple 2014-07-23 Link ATB
19988 C25H32O21 (2R)-2-{[(2S)-2-{[(2R)-2-{[(2S ... 5_plga_test 78 0 multiple 2014-07-23 Link ATB
19987 C21H28N7O14P2 1-[(2S,3R,4S,5S)-5-({[(S)-{[(R ... 70 -1 multiple 2014-07-23 Link ATB
19985 C47H74NO17 AMB 138 0 multiple 2014-07-22 Link ATB
19984 C10H16N2O3S 5-[(3aR,4R,6aS)-2-oxo-hexahydr ... biotin 32 0 multiple 2014-07-22 Link ATB
19983 C76H53N3O32 humic acid 157 -3 multiple 2014-07-22 Link Partial
19981 C60H8O6 fullerol6 72 0 multiple 2014-07-22 Link ATB
19978 HO4P 3-hydroxy-1,2,3λ5-dioxapho ... POB 5 -1 multiple 2014-07-22 Link ATB
19977 H2O water OH 2 -1 multiple 2014-07-22 Link ATB
19976 H3O4P trihydroxy(oxo)-λ4-phospha ... POB 6 -2 multiple 2014-07-22 Link ATB
19975 H3O4P trihydroxy(oxo)-λ4-phospha ... POA 5 -3 multiple 2014-07-22 Link ATB
19973 C12H22O11 (2R,3R,4R,5S,6R)-6-(hydroxymet ... maltose disaccharide 45 0 multiple 2014-07-21 Link ATB
19972 H3O4P (trihydroxy-λ5-phosphanyli ... h2p 7 -1 multiple 2014-07-21 Link ATB
19971 H3O4P trihydroxy(oxo)-λ4-phospha ... hpo 6 -2 multiple 2014-07-21 Link ATB
19970 C66H134O34 3,6,9,12,15,18,21,24,27,30,33, ... peg 234 0 multiple 2014-07-21 Link ATB
19969 C62H111N11O12 (3S,6S,9S,12R,15S,18S,21S,24S, ... 1 196 0 multiple 2014-07-21 Link ATB
19968 C21H20O6 2-methoxy-4-[(1E,4Z,6E)-7-(3-m ... curcumin 47 0 multiple 2014-07-21 Link ATB
19967 C76H146N8O21 2-{N-[(2S)-2-ethylhexyl]-2-{N- ... 251 0 multiple 2014-07-20 Link ATB
19966 C3H2F6O 1,1,1,3,3,3-hexafluoropropan-2 ... hfip 12 0 multiple 2014-07-20 Link ATB
19965 C34H29F2N3O3 (2'R,3R,7'aR)-2'-{[(3Z,5E)-3,5 ... 71 0 multiple 2014-07-20 Link ATB
19964 C34H57F2N3O3 (2R,2'R,3S,3aS,7aR,7'aR)-2'-[( ... 99 0 multiple 2014-07-20 Link ATB
19963 C120H24 Single Wall Carbon nanotube 120 0 multiple 2014-07-20 Link ATB
19962 C9H12O 2-propylbenzen-1-olate 22 0 multiple 2014-07-19 Link ATB
19956 C39H52O7 (1S,3R)-3-hydroxy-4-[(1P,3E,5E ... 96 0 multiple 2014-07-19 Link ATB
19951 C39H50O7 (1S,3R)-3-hydroxy-4-[(1P,3E,5E ... peridinin 96 0 multiple 2014-07-18 Link ATB
19950 C9H17O8P [(2R)-2,3-bis(propanoyloxy)pro ... LipidBuilder-testBB 35 0 multiple 2014-07-18 Link ATB
19949 C10H20O3 2-hydroxyethyl octanoate LipidBuilder-testTail 33 0 multiple 2014-07-18 Link ATB
19948 C4H13NO5P 2-{[(S)-(2-aminoethoxy)(hydrox ... LipidBuilder-testHG 23 0 multiple 2014-07-18 Link ATB
19946 C14H18FN5O3 (2R)-1-(dimethylamino)-3-{4-[( ... 584_2 42 1 multiple 2014-07-18 Link ATB
19945 C14H18FN5O3 (2R)-1-(dimethylamino)-3-{4-[( ... 584_1 42 1 multiple 2014-07-18 Link ATB
19944 C6H8N 1-methylpyridine 15 1 multiple 2014-07-18 Link ATB
19943 C14H18FN5O3 (2R)-1-(dimethylamino)-3-{4-[( ... 584_pose2 42 1 multiple 2014-07-17 Link ATB
19942 C14H18FN5O3 (2R)-1-(dimethylamino)-3-{4-[( ... 584_pose1 42 1 multiple 2014-07-17 Link ATB
19941 C14H18FN5O3 (2R)-1-(dimethylamino)-3-{4-[( ... 42 1 multiple 2014-07-17 Link ATB
19937 C14H18FN5O3 (2R)-1-(dimethylamino)-3-{4-[( ... 41 0 multiple 2014-07-17 Link ATB
19936 C35H38Cl2N8O4 1-[(2R)-butan-2-yl]-4-{4-[4-(4 ... IYN 87 0 multiple 2014-07-17 Link ATB
19935 C16H14F3N5O (2R,3S)-2-(2,4-difluorophenyl) ... VOR 39 0 multiple 2014-07-17 Link ATB
19930 C39H56O7 (1S,3R,4S)-3-hydroxy-4-[(2E,5E ... pid 98 0 multiple 2014-07-17 Link ATB
19927 C22H19ClO3 1,4-dioxo-3-[(1s,4s)-4-(4-chlo ... 45 0 multiple 2014-07-17 Link ATB
19925 C15H23Cl2NO5 3-[(2S,4S,5R)-5,6-dichloro-2,4 ... 44 0 multiple 2014-07-17 Link ATB
19920 C26H16N2 5-(2-phenylethynyl)-2-[5-(2-ph ... 5,5-Bis(phenylethynyl)-2,2-b ... 44 0 multiple 2014-07-16 Link ATB
19919 C40H52 1,3,3-trimethyl-2-[(1E,3E,5E,7 ... caroten 92 0 multiple 2014-07-15 Link ATB
19914 C42H70O35 (1S,3R,5R,6S,8R,10R,11S,13R,15 ... beta-cyclodextrin 147 0 multiple 2014-07-15 Link ATB
<< previous page
next page >>

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.