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)CSN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge0
Forcefieldmultiple
Molecule ID17429
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 Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:17
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 
2747 None - 20 0 Manual* N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17492 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
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
581 None - 16 0 Manual* N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17313 None - 32 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)