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 ID17331
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 
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
17304 None - 25 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
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17183 None - 23 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
17490 None - 22 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17453 None - 28 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17237 None - 16 -1 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)