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 
17202 None - 33 1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17187 None - 15 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 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)