MD Topology | NMR | X-Ray

Visualize with JSmol

Processing Information

QM Processing Stage

Click table to toggle details.

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)TOL
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge0
Forcefieldmultiple
Molecule ID583
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 21:53:46
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
Oostenbrink, Villa, Mark and V ... 343 toluene Rectangular box; 343 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 
17160 None - 20 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17350 None - 15 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17366 None - 29 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
Previous Page Next Page

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)