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)YCH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge0
Forcefieldmultiple
Molecule ID17533
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:19
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 
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
1583 None - 125 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
174 None - 19 -1 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 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
17412 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 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
17274 None - 24 -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)