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 (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 
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17486 None - 21 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17518 None - 28 0 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
1733 None - 81 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)