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)S2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms17
Net Charge-2
Forcefieldmultiple
Molecule ID17329
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 Version54A7 (IFP54A7.dat / 54A7.ifp)
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
2752 None - 19 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17266 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
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17281 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
17166 None - 27 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17535 None - 24 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)