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 
6451 None - 27 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
2671 None - 47 -3 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
1649 None - 5 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
2920 None - 27 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
1679 None - 31 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
2002 None - 24 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
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
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
1611 None - 18 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
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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)