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 Typelipid
Residue Name (RNME)POPC
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms134
Net Charge0
Forcefieldmultiple
Molecule ID1506
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

United-Atom G96 (optimised geometry)

Consistency Check of Topology

Check Top Result for GROMOS96 United-Atom Topology

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2010-07-08 11:44:56
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
David Poger POPC bilayer Hydrated 128-POPC bilayer Link
Megan O'Mara P-gp with NCP, ATP in a Choles ... P-gp with NCP, ATP in a Choles ... Link
ZhiGuang Jia, Megan L. O'Mara, ... Vancomycin and lipid II forms ... Vancomycin spontenoursly attac ... 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
ZG Jia, ML O'Mara, J Zuegg, MA ... Lipid II in POPC membrane System contain 3 lipid II and ... 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 
1577 None - 138 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17272 None - 18 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17154 None - 17 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)