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)T2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge-2
Forcefieldmultiple
Molecule ID17346
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 13:07:16
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 
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
17371 None - 18 -1 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
17413 None - 24 1 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
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
17249 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
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
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
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
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
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
17271 None - 18 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17420 None - 21 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)