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 Typeamino acid
Residue Name (RNME)KCN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID17231
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 13:07:15
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 
6459 None - 16 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17327 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
2920 None - 27 1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17175 None - 25 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17222 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
17529 None - 18 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
580 None - 12 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
1605 None - 23 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)