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) 2000 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)K2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-2
Forcefieldmultiple
Molecule ID17247
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 13:07:15
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 
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 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
18619 None - 49 -3 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 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
562 None - 9 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17485 None - 21 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17517 None - 28 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17249 None - 23 -2 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
1567 None - 119 0 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17197 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
5031 None - 78 0 Manual* N/A Compare with
17449 None - 23 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17483 None - 15 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17515 None - 26 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
171 None - 14 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)