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)DN3
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms17
Net Charge0
Forcefieldmultiple
Molecule ID17287
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 
17447 None - 28 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 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
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
17209 None - 27 -2 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17177 None - 20 -1 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
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
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 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
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
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
17316 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
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
17427 None - 34 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17311 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
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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)