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)F3H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge0
Forcefieldmultiple
Molecule ID17318
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17417 None - 21 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
17350 None - 15 0 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17382 None - 23 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17298 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
17183 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
17215 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
17306 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
17191 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
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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)