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)2PTL
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID3411
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 Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2011-07-28 17:47:26
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
Horta, Fuchs, Van Gunsteren an ... 512 2-pentanol 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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
3505 None - 18 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17340 None - 18 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17198 None - 26 1 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)