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 
17403 None - 16 -1 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17164 None - 23 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17177 None - 20 -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)