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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) | KH5 |
Formula | None |
IUPAC InChI Key | None |
IUPAC InChI | None |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | NULL |
Number of atoms | 25 |
Net Charge | 0 |
Forcefield | multiple |
Molecule ID | 17437 |
Visibility | Public |
Molecule Tags |
Force Field Version | 54A7 (IFP54A7.dat / 54A7.ifp) |
Upload Date | 2014-02-03 13:07:17 |
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 |
---|---|---|---|---|---|---|---|
5797 | None | - | 18 | -1 | Manual* | N/A | Compare with |
1611 | None | - | 18 | 0 | Manual* | N/A | Compare with |
17155 | None | - | 17 | 0 | Manual | N/A | Compare with |
17308 | None | - | 23 | 0 | Manual | N/A | Compare with |
17340 | None | - | 18 | 0 | Manual | N/A | Compare with |
17462 | None | - | 22 | 0 | Manual | N/A | Compare with |
17494 | None | - | 19 | 0 | Manual | N/A | Compare with |
565 | None | - | 9 | 0 | Manual* | N/A | Compare with |
17225 | None | - | 20 | 0 | Manual | N/A | Compare with |
17257 | None | - | 15 | -1 | Manual | N/A | Compare with |
17410 | None | - | 18 | 0 | Manual | N/A | Compare with |
17443 | None | - | 28 | 1 | Manual | N/A | Compare with |
2002 | None | - | 24 | 0 | Manual* | N/A | Compare with |
17174 | None | - | 25 | 0 | Manual | N/A | Compare with |
3505 | None | - | 18 | 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 |
1566 | None | - | 129 | 0 | Manual* | N/A | Compare with |
17425 | None | - | 34 | 1 | Manual | N/A | Compare with |
17458 | None | - | 28 | 0 | Manual | N/A | Compare with |
2919 | None | - | 52 | -1 | 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 |
1547 | None | - | 24 | 0 | Manual* | N/A | Compare with |
21025 | None | - | 209 | -4 | Manual* | N/A | Compare with |
4582 | None | - | 161 | -8 | Manual* | N/A | Compare with |
1587 | None | - | 155 | 0 | Manual* | N/A | Compare with |
7283 | None | - | 87 | 1 | Manual* | N/A | Compare with |
17291 | None | - | 28 | 0 | Manual | N/A | Compare with |
17323 | None | - | 18 | 0 | Manual | N/A | Compare with |
17477 | None | - | 27 | -1 | Manual | N/A | Compare with |
177 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17509 | None | - | 27 | 0 | Manual | N/A | Compare with |
581 | None | - | 16 | 0 | Manual* | N/A | Compare with |
17240 | None | - | 16 | -1 | Manual | N/A | Compare with |
17272 | None | - | 18 | 0 | Manual | N/A | Compare with |
17153 | None | - | 17 | 0 | Manual | N/A | Compare with |
17306 | None | - | 23 | 0 | Manual | N/A | Compare with |
17338 | None | - | 18 | 0 | Manual | N/A | Compare with |
17492 | None | - | 22 | 0 | Manual | N/A | Compare with |
562 | None | - | 9 | 0 | Manual* | N/A | Compare with |
17255 | None | - | 27 | 0 | Manual | N/A | Compare with |
17408 | None | - | 28 | -1 | Manual | N/A | Compare with |
17441 | None | - | 28 | 1 | Manual | N/A | Compare with |
1738 | None | - | 77 | 0 | Manual* | N/A | Compare with |
17172 | None | - | 28 | 0 | Manual | N/A | Compare with |
3502 | None | - | 19 | 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 |
1564 | None | - | 143 | 0 | Manual* | N/A | Compare with |
5795 | None | - | 18 | -1 | Manual* | N/A | Compare with |
1606 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17456 | None | - | 28 | 0 | Manual | N/A | Compare with |
2749 | None | - | 14 | 0 | Manual* | N/A | Compare with |
17187 | None | - | 15 | 0 | Manual | N/A | Compare with |
17219 | None | - | 31 | 1 | Manual | N/A | Compare with |
17372 | None | - | 18 | -1 | Manual | N/A | Compare with |
17526 | None | - | 18 | 0 | Manual | N/A | Compare with |
1539 | None | - | 137 | 0 | Manual* | N/A | Compare with |
18660 | None | - | 49 | -3 | Manual* | N/A | Compare with |
1584 | None | - | 137 | 0 | Manual* | N/A | Compare with |
7281 | None | - | 62 | 1 | Manual* | N/A | Compare with |
17289 | None | - | 28 | 0 | Manual | N/A | Compare with |
17321 | None | - | 18 | 0 | Manual | N/A | Compare with |
17475 | None | - | 23 | 0 | Manual | N/A | Compare with |
175 | None | - | 19 | 0 | Manual* | N/A | Compare with |
17507 | None | - | 29 | 0 | Manual | N/A | Compare with |
578 | None | - | 10 | 0 | Manual* | N/A | Compare with |
17238 | None | - | 16 | -1 | Manual | N/A | Compare with |
17270 | None | - | 18 | 0 | Manual | N/A | Compare with |
17423 | None | - | 21 | 0 | Manual | N/A | Compare with |
17304 | None | - | 25 | 0 | Manual | N/A | Compare with |
17336 | None | - | 30 | 1 | Manual | N/A | Compare with |
17490 | None | - | 22 | 0 | Manual | N/A | Compare with |
215 | None | - | 19 | 0 | Manual* | N/A | Compare with |
17253 | None | - | 27 | 0 | Manual | N/A | Compare with |
17406 | None | - | 28 | -1 | Manual | N/A | Compare with |
17439 | None | - | 25 | 0 | Manual | N/A | Compare with |
1733 | None | - | 81 | 0 | Manual* | N/A | Compare with |
17170 | None | - | 28 | 0 | Manual | N/A | Compare with |
3500 | None | - | 18 | 0 | Manual* | N/A | Compare with |
17202 | None | - | 33 | 1 | Manual | N/A | Compare with |
17355 | None | - | 23 | 0 | Manual | N/A | Compare with |
17387 | None | - | 20 | -2 | Manual | N/A | Compare with |
17541 | None | - | 29 | 0 | Manual | N/A | Compare with |
1562 | None | - | 125 | 0 | Manual* | N/A | Compare with |
5471 | None | - | 130 | -10 | Manual* | N/A | Compare with |
1604 | None | - | 16 | 0 | Manual* | N/A | Compare with |
17151 | None | - | 16 | -1 | Manual | N/A | Compare with |
2745 | None | - | 24 | 0 | Manual* | N/A | Compare with |
17185 | None | - | 15 | 0 | Manual | N/A | Compare with |
4581 | None | - | 161 | -8 | Manual* | N/A | Compare with |
17217 | None | - | 31 | 1 | Manual | N/A | Compare with |
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.