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 
17487 None - 21 0 Manual N/A Compare with
1594 None - 10 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
1563 None - 137 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
1605 None - 23 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
17233 None - 26 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
174 None - 19 -1 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
1560 None - 123 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
1602 None - 20 0 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
17230 None - 27 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
1570 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
1646 None - 3 0 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
1526 None - 143 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)