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)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 ID17247
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17355 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)