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)DN3
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms17
Net Charge0
Forcefieldmultiple
Molecule ID17287
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 13:07:16
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
4578 None - 161 -8 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17461 None - 22 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17193 None - 28 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)