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 building block
Residue Name (RNME)F23
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17302
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 Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:16
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 
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
1733 None - 81 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 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
1532 None - 149 0 Manual* N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 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
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17290 None - 28 0 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)