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)TOX
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge0
Forcefieldmultiple
Molecule ID17187
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 13:07:14
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 
1552 None - 149 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17350 None - 15 0 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17382 None - 23 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17513 None - 26 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17347 None - 20 -2 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)