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)MSX
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge0
Forcefieldmultiple
Molecule ID17400
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:17
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 
17316 None - 32 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
574 None - 17 0 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
572 None - 17 0 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17378 None - 28 -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)