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)YCH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge0
Forcefieldmultiple
Molecule ID17535
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 13:07:19
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 
17261 None - 17 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17512 None - 27 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17510 None - 27 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
165 None - 26 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)