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 building block
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 ID17352
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 
17194 None - 28 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
2920 None - 27 1 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17342 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
17258 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
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
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
17253 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
17295 None - 9 -1 Manual N/A Compare with
17327 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
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
17337 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
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
17290 None - 28 0 Manual N/A Compare with
17322 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
17365 None - 29 0 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -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)