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 ID17451
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 13:07:18
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17336 None - 30 1 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17430 None - 15 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
570 None - 11 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)