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) 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 Typeamino acid building block
Residue Name (RNME)QME
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17284
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS11 Files

Topology Files Structure Files
GROMOS11 United-Atom MTB
United-Atom PDB (optimised geometry)

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:16
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

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 
1540 None - 143 0 Manual* N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17382 None - 23 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17499 None - 25 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17448 None - 28 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17497 None - 25 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17429 None - 15 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17226 None - 20 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)