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)NME
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge0
Forcefieldmultiple
Molecule ID17228
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

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 
17214 None - 29 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17295 None - 9 -1 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)