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)P3H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17207
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 13:07:15
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 
9371 None - 11 -2 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17505 None - 29 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17168 None - 27 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 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
7284 None - 71 1 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17518 None - 28 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17250 None - 23 -2 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)