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) 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)NMA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms12
Net Charge0
Forcefieldmultiple
Molecule ID582
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 21:52:01
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
Oostenbrink, Villa, Mark and V ... 512 N-methylacetamide 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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1511 None - 131 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
1601 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)