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)K2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-2
Forcefieldmultiple
Molecule ID17247
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 
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
17423 None - 21 0 Manual N/A Compare with
17307 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
17349 None - 15 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 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
1510 None - 161 0 Manual* N/A Compare with
17492 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
17227 None - 20 0 Manual N/A Compare with
17260 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
17445 None - 28 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 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
17339 None - 18 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17255 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
17413 None - 24 1 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
17366 None - 29 0 Manual N/A Compare with
17250 None - 23 -2 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
17408 None - 28 -1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 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
17361 None - 12 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17277 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
17551 None - 15 -1 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 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
17504 None - 32 0 Manual N/A Compare with
17356 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)