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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
4602 None - 113 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17207 None - 18 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17222 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
17529 None - 18 0 Manual N/A Compare with
30988 None - 1456 0 Template N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17205 None - 18 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
18675 None - 140 -3 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)