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 
17263 None - 17 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17416 None - 24 1 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17448 None - 28 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17431 None - 15 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17414 None - 24 1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17512 None - 27 0 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17429 None - 15 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17412 None - 18 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1642 None - 18 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)