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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17159 None - 20 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17338 None - 18 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17442 None - 28 1 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)