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)NH3
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17339
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:16
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 
17145 None - 33 1 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
3505 None - 18 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
1566 None - 129 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
565 None - 9 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
1547 None - 24 0 Manual* N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17313 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
17262 None - 17 0 Manual N/A Compare with
17416 None - 24 1 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
3502 None - 19 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
1564 None - 143 0 Manual* N/A Compare with
1606 None - 20 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
562 None - 9 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17311 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
17260 None - 15 -1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1539 None - 137 0 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
3500 None - 18 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
1562 None - 125 0 Manual* N/A Compare with
1604 None - 16 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
215 None - 19 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
5798 None - 19 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)