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) 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 Typeamino acid building block
Residue Name (RNME)ABZ
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms17
Net Charge0
Forcefieldmultiple
Molecule ID1603
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 Date2010-07-20 13:51:03
Literature ReferenceLink

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 
17173 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17424 None - 21 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17439 None - 25 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17422 None - 21 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17437 None - 25 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
2920 None - 27 1 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)