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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 |
Current Processing State | Completed |
Total Processing Time | NA (hh:mm:ss) |
Molecule Type | amino acid |
Residue Name (RNME) | H12 |
Formula | None |
IUPAC InChI Key | None |
IUPAC InChI | None |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | NULL |
Number of atoms | 23 |
Net Charge | -2 |
Forcefield | multiple |
Molecule ID | 17249 |
Visibility | Public |
Molecule Tags |
Force Field Version | 54A7 (IFP54A7.dat / 54A7.ifp) |
Upload Date | 2014-02-03 13:07:15 |
Literature Reference | Drazen 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 |
Compare All Topologies (633)RMSD Matrix (633)
Molid | Formula | Iupac | Atoms | Charge | Curation | Δ Qm Optimized Energy (kJ.mol-1) | Compare |
---|---|---|---|---|---|---|---|
17272 | None | - | 18 | 0 | Manual | N/A | Compare with |
17241 | None | - | 26 | -1 | Manual | N/A | Compare with |
17274 | None | - | 24 | -1 | Manual | N/A | Compare with |
17243 | None | - | 26 | -1 | Manual | N/A | Compare with |
17276 | None | - | 24 | -1 | Manual | N/A | Compare with |
17245 | None | - | 27 | -2 | Manual | N/A | Compare with |
17278 | None | - | 24 | 1 | Manual | N/A | Compare with |
17247 | None | - | 27 | -2 | Manual | N/A | Compare with |
17280 | None | - | 24 | 1 | Manual | N/A | Compare with |
17250 | None | - | 23 | -2 | Manual | N/A | Compare with |
17282 | None | - | 23 | 0 | Manual | N/A | Compare with |
17252 | None | - | 23 | -2 | Manual | N/A | Compare with |
17254 | None | - | 27 | 0 | Manual | N/A | Compare with |
17256 | None | - | 27 | 0 | Manual | N/A | Compare with |
17225 | None | - | 20 | 0 | Manual | N/A | Compare with |
17258 | None | - | 15 | -1 | Manual | N/A | Compare with |
17227 | None | - | 20 | 0 | Manual | N/A | Compare with |
17260 | None | - | 15 | -1 | Manual | N/A | Compare with |
17229 | None | - | 27 | 0 | Manual | N/A | Compare with |
17262 | None | - | 17 | 0 | Manual | N/A | Compare with |
17231 | None | - | 27 | 0 | Manual | N/A | Compare with |
17264 | None | - | 17 | 0 | Manual | N/A | Compare with |
17233 | None | - | 26 | 0 | Manual | N/A | Compare with |
17266 | None | - | 19 | 0 | Manual | N/A | Compare with |
17235 | None | - | 26 | 0 | Manual | N/A | Compare with |
17268 | None | - | 19 | 0 | Manual | N/A | Compare with |
17237 | None | - | 16 | -1 | Manual | N/A | Compare with |
17270 | None | - | 18 | 0 | Manual | N/A | Compare with |
17239 | None | - | 16 | -1 | Manual | N/A | Compare with |
17332 | None | - | 17 | -2 | Manual | N/A | Compare with |
17302 | None | - | 25 | 0 | Manual | N/A | Compare with |
17334 | None | - | 30 | 1 | Manual | N/A | Compare with |
17304 | None | - | 25 | 0 | Manual | N/A | Compare with |
17336 | None | - | 30 | 1 | Manual | N/A | Compare with |
17306 | None | - | 23 | 0 | Manual | N/A | Compare with |
17338 | None | - | 18 | 0 | Manual | N/A | Compare with |
17308 | None | - | 23 | 0 | Manual | N/A | Compare with |
17340 | None | - | 18 | 0 | Manual | N/A | Compare with |
17310 | None | - | 25 | -1 | Manual | N/A | Compare with |
17342 | None | - | 23 | -2 | Manual | N/A | Compare with |
17312 | None | - | 25 | -1 | Manual | N/A | Compare with |
17314 | None | - | 32 | 0 | Manual | N/A | Compare with |
17284 | None | - | 23 | 0 | Manual | N/A | Compare with |
17316 | None | - | 32 | 0 | Manual | N/A | Compare with |
17286 | None | - | 17 | 0 | Manual | N/A | Compare with |
17318 | None | - | 24 | 0 | Manual | N/A | Compare with |
17288 | None | - | 17 | 0 | Manual | N/A | Compare with |
17320 | None | - | 24 | 0 | Manual | N/A | Compare with |
17290 | None | - | 28 | 0 | Manual | N/A | Compare with |
17322 | None | - | 18 | 0 | Manual | N/A | Compare with |
17292 | None | - | 28 | 0 | Manual | N/A | Compare with |
17324 | None | - | 18 | 0 | Manual | N/A | Compare with |
17294 | None | - | 9 | -1 | Manual | N/A | Compare with |
17326 | None | - | 25 | 0 | Manual | N/A | Compare with |
17296 | None | - | 9 | -1 | Manual | N/A | Compare with |
17328 | None | - | 25 | 0 | Manual | N/A | Compare with |
17298 | None | - | 18 | 0 | Manual | N/A | Compare with |
17330 | None | - | 17 | -2 | Manual | N/A | Compare with |
17300 | None | - | 18 | 0 | Manual | N/A | Compare with |
17392 | None | - | 18 | 0 | Manual | N/A | Compare with |
17362 | None | - | 12 | 0 | Manual | N/A | Compare with |
17394 | None | - | 24 | -1 | Manual | N/A | Compare with |
17364 | None | - | 12 | 0 | Manual | N/A | Compare with |
17396 | None | - | 24 | -1 | Manual | N/A | Compare with |
17366 | None | - | 29 | 0 | Manual | N/A | Compare with |
17398 | None | - | 21 | 0 | Manual | N/A | Compare with |
17368 | None | - | 29 | 0 | Manual | N/A | Compare with |
17400 | None | - | 21 | 0 | Manual | N/A | Compare with |
17370 | None | - | 18 | -1 | Manual | N/A | Compare with |
17372 | None | - | 18 | -1 | Manual | N/A | Compare with |
17374 | None | - | 30 | -1 | Manual | N/A | Compare with |
17344 | None | - | 23 | -2 | Manual | N/A | Compare with |
17376 | None | - | 30 | -1 | Manual | N/A | Compare with |
17346 | None | - | 20 | -2 | Manual | N/A | Compare with |
17378 | None | - | 28 | -1 | Manual | N/A | Compare with |
17348 | None | - | 20 | -2 | Manual | N/A | Compare with |
17380 | None | - | 28 | -1 | Manual | N/A | Compare with |
17350 | None | - | 15 | 0 | Manual | N/A | Compare with |
17382 | None | - | 23 | 0 | Manual | N/A | Compare with |
17352 | None | - | 15 | 0 | Manual | N/A | Compare with |
17384 | None | - | 23 | 0 | Manual | N/A | Compare with |
17354 | None | - | 23 | 0 | Manual | N/A | Compare with |
17386 | None | - | 20 | -2 | Manual | N/A | Compare with |
17356 | None | - | 23 | 0 | Manual | N/A | Compare with |
17388 | None | - | 20 | -2 | Manual | N/A | Compare with |
17358 | None | - | 30 | 0 | Manual | N/A | Compare with |
17390 | None | - | 18 | 0 | Manual | N/A | Compare with |
17360 | None | - | 30 | 0 | Manual | N/A | Compare with |
17452 | None | - | 23 | 0 | Manual | N/A | Compare with |
17422 | None | - | 21 | 0 | Manual | N/A | Compare with |
566 | None | - | 12 | 0 | Manual* | N/A | Compare with |
165 | None | - | 26 | 0 | Manual* | N/A | Compare with |
17454 | None | - | 28 | 0 | Manual | N/A | Compare with |
17424 | None | - | 21 | 0 | Manual | N/A | Compare with |
568 | None | - | 16 | 0 | Manual* | N/A | Compare with |
167 | None | - | 14 | -1 | Manual* | N/A | Compare with |
17456 | None | - | 28 | 0 | Manual | N/A | Compare with |
17426 | None | - | 34 | 1 | Manual | N/A | Compare with |
570 | None | - | 11 | 0 | Manual* | N/A | Compare with |
169 | None | - | 13 | 0 | Manual* | N/A | Compare with |
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The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.