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)NME
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge0
Forcefieldmultiple
Molecule ID17227
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 13:07:15
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 
17461 None - 22 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17338 None - 18 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
5639 None - 127 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)