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 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 (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 
17476 None - 23 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
7281 None - 62 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)