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)CSE
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms16
Net Charge-1
Forcefieldmultiple
Molecule ID17152
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 13:07:14
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
4604 None - 217 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
584 None - 15 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17236 None - 26 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)