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)KPH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge1
Forcefieldmultiple
Molecule ID17547
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 13:07:19
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 
17518 None - 28 0 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17512 None - 27 0 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17542 None - 29 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)