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 
17355 None - 23 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17168 None - 27 0 Manual N/A Compare with
582 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
6451 None - 27 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17368 None - 29 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
1586 None - 149 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
176 None - 20 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17264 None - 17 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)