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)WKF
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms29
Net Charge0
Forcefieldmultiple
Molecule ID17506
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 Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:18
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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge > Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17379 None - 28 -1 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
562 None - 9 0 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
619 None - 16 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1606 None - 20 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)