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 building block
Residue Name (RNME)CYH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge0
Forcefieldmultiple
Molecule ID17484
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 13:07:18
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 
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
17460 None - 28 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17493 None - 19 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1606 None - 20 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
567 None - 10 0 Manual* N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17440 None - 25 0 Manual N/A Compare with
1601 None - 17 0 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
17482 None - 15 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17505 None - 29 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17295 None - 9 -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)