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 
9371 None - 11 -2 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17168 None - 27 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17249 None - 23 -2 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)