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)KH5
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17437
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 Version54A7 (IFP54A7.dat / 54A7.ifp)
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 
17157 None - 20 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17494 None - 19 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17410 None - 18 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 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
17342 None - 23 -2 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17272 None - 18 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17338 None - 18 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17492 None - 22 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 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)