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)KPH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge1
Forcefieldmultiple
Molecule ID17545
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 13:07:19
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 
4580 None - 161 -8 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17174 None - 25 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
17544 None - 29 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 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
2694 None - 77 -3 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
177 None - 20 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
581 None - 16 0 Manual* N/A Compare with
7283 None - 87 1 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
17508 None - 29 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
578 None - 10 0 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 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)