MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

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Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 1000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information

Molecule Typeheteromolecule
Residue Name (RNME)MEE
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms11
Net Charge0
Forcefieldmultiple
Molecule ID570
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS96 Files

Topology Files Structure Files
GROMOS96 United-Atom MTB
GROMOS96 United-Atom Topology
United-Atom PDB (optimised geometry)

Additional Structure Files

Files
United-Atom G96 (optimised geometry)

Consistency Check of Topology

Files
Check Top Result for GROMOS96 United-Atom Topology

Topology Information

Force Field Version53A5 (IFP53A5.dat)
Upload Date2009-09-25 21:22:50
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
Oostenbrink, Villa, Mark and V ... 512 methyl ethyl ester Rectangular box; 512 molecules Link

Topology History

Other conformers for this molecule (1-100 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac > Atoms  Charge  Curation  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17293 None - 9 -1 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17483 None - 15 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17362 None - 12 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
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ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)