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 ID17548
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 
17493 None - 19 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
1502 None - 106 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)