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 Typesolvent
Residue Name (RNME)H2O
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms3
Net Charge0
Forcefieldmultiple
Molecule ID1596
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS96 Files

Topology Files Structure Files
GROMOS96 United-Atom MTB

Topology Information

Force Field Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2010-07-19 10:01:45
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
David Poger DPPC bilayer Hydrated 128-DPPC bilayer Link
Megan O'Mara Membrane-embedded P-glycoprote ... central P-gp structure from 30 ... Link
Megan L. O'Mara ATP-bound P-gp inward facing, ... P-gp with Mg2+ and ATP in a PO ... Link
Megan L. O'Mara Membrane-embedded P-gp with AT ... P-gp with Mg2+ and ATP in a PO ... Link
Megan L. O'Mara ATP-bound P-gp asymmetric memb ... P-gp with Mg2+ and ATP in a PO ... Link
Megan L. O'Mara ATP-bound P-gp asymmetric memb ... P-gp with Mg2+ and ATP in a PO ... 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 
1606 None - 20 0 Manual* N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17314 None - 32 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17363 None - 12 0 Manual N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17327 None - 25 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)