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 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

Files
United-Atom G96 (optimised geometry)

Consistency Check of Topology

Files
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 
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
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
4908 None - 40 -4 Manual* N/A Compare with
17350 None - 15 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17505 None - 29 0 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
1560 None - 123 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
1570 None - 125 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
17374 None - 30 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17422 None - 21 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)