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)YNB
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge0
Forcefieldmultiple
Molecule ID17516
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 (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 
17198 None - 26 1 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17248 None - 27 -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)