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)K3C
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms34
Net Charge1
Forcefieldmultiple
Molecule ID17428
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 13:07:17
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 (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac > Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17162 None - 23 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
4581 None - 161 -8 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)