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
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 13:07:17
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 
17155 None - 17 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17420 None - 21 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17487 None - 21 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17382 None - 23 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17485 None - 21 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
5471 None - 130 -10 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)