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)K2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-2
Forcefieldmultiple
Molecule ID17246
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
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 
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17417 None - 21 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17432 None - 15 0 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17381 None - 23 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17415 None - 24 1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17430 None - 15 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17413 None - 24 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17428 None - 34 1 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17460 None - 28 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)