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)KPH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge1
Forcefieldmultiple
Molecule ID17546
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 13:07:19
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 (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 
582 None - 12 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17489 None - 22 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17541 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)