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 Typeheteromolecule
Residue Name (RNME)3PTL
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID3412
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 Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2011-07-28 17:53:22
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
Horta, Fuchs, Van Gunsteren an ... 512 3-pentanol Rectangular box; 512 molecules 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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1524 None - 137 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
2920 None - 27 1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17161 None - 23 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
6459 None - 16 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17163 None - 23 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
1588 None - 125 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)