MD Topology | NMR | X-Ray

Visualize with JSmol

Processing Information

QM Processing Stage

Click table to toggle details.

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

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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula > Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17219 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17168 None - 27 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17519 None - 28 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
Previous Page Next Page

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)