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 building block
Residue Name (RNME)K3C
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms34
Net Charge1
Forcefieldmultiple
Molecule ID17428
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:17
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 
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17389 None - 18 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
4579 None - 161 -8 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
1525 None - 147 0 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 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
17454 None - 28 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17368 None - 29 0 Manual N/A Compare with
570 None - 11 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)

Column Lengths: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] Column Lengths: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] Column Lengths: [4, 4, 4, 4] Column Lengths: [3, 3, 3, 3] Column Lengths: [3, 3, 3]