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)PYA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms9
Net Charge-1
Forcefieldmultiple
Molecule ID17296
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 13:07:16
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 
582 None - 12 0 Manual* N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1506 None - 134 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)