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 
6458 None - 13 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
2920 None - 27 1 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17370 None - 18 -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)