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)POH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms12
Net Charge0
Forcefieldmultiple
Molecule ID566
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 Version53A5 (IFP53A5.dat)
Upload Date2009-09-25 21:14:56
Literature ReferenceLink

Affiliated Pre-Equilibrated Systems

Author Name Description Link
Oostenbrink, Villa, Mark and V ... 512 2-propanol 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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
3485 None - 6 0 Manual* N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17423 None - 21 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17418 None - 21 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
17413 None - 24 1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
1538 None - 161 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)