MD Topology | NMR | X-Ray

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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) 2000 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 (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid > Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare >
17361 None - 12 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17262 None - 17 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)