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 building block
Residue Name (RNME)KCA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge-1
Forcefieldmultiple
Molecule ID17242
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 13:07:15
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 
17281 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17301 None - 25 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)