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)KCN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID17231
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 
1560 None - 123 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17506 None - 29 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 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
1525 None - 147 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17489 None - 22 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
6461 None - 15 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
211 None - 14 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17236 None - 26 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
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 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
1577 None - 138 0 Manual* N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17487 None - 21 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17519 None - 28 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17404 None - 16 -1 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
208 None - 23 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17234 None - 26 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
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
1555 None - 167 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
1595 None - 5 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)