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) 1000 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)CSE
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms16
Net Charge-1
Forcefieldmultiple
Molecule ID17151
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS11 Files

Topology Files Structure Files
GROMOS11 United-Atom MTB
United-Atom PDB (optimised geometry)

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:14
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
3412 None - 18 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17272 None - 18 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17427 None - 34 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)