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)GSA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17410
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 
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17453 None - 28 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17423 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
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
17450 None - 23 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)