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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) | 2000 | 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 |
Current Processing State | Completed |
Total Processing Time | NA (hh:mm:ss) |
Molecule Type | lipid |
Residue Name (RNME) | POPC |
Formula | None |
IUPAC InChI Key | None |
IUPAC InChI | None |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | NULL |
Number of atoms | 134 |
Net Charge | 0 |
Forcefield | multiple |
Molecule ID | 1506 |
Visibility | Public |
Molecule Tags |
Force Field Version | 54A7 (IFP54A7.dat / 54A7.ifp) |
Upload Date | 2010-07-08 11:44:56 |
Literature Reference | Link |
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 |