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)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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17237 None - 16 -1 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17391 None - 18 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)