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
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

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 
168 None - 15 0 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
571 None - 14 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
17516 None - 26 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 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
17448 None - 28 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17314 None - 32 0 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
17230 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
569 None - 8 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
17514 None - 26 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17245 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
17194 None - 28 0 Manual N/A Compare with
1572 None - 153 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
4604 None - 217 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17395 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
205 None - 24 0 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
619 None - 16 0 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
2749 None - 14 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17446 None - 28 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
1733 None - 81 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17243 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
17192 None - 44 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17378 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
164 None - 27 1 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17207 None - 18 0 Manual N/A Compare with
1589 None - 131 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
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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)