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)H1M
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17449
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 13:07:18
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 
17261 None - 17 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17336 None - 30 1 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17432 None - 15 0 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17365 None - 29 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)