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)TDH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge0
Forcefieldmultiple
Molecule ID17351
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 13:07:16
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
3412 None - 18 0 Manual* N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17423 None - 21 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17306 None - 23 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17418 None - 21 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
17413 None - 24 1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
1532 None - 149 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)