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)MXS
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge0
Forcefieldmultiple
Molecule ID17420
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 13:07:17
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1581 None - 149 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17161 None - 23 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)