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)R0P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms31
Net Charge0
Forcefieldmultiple
Molecule ID17467
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 13:07:18
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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17552 None - 15 -1 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17417 None - 21 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)