MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

Click table to toggle details.

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) 2000 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)HTY
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17173
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:14
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 (301-400 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17334 None - 30 1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
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
17342 None - 23 -2 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
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
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
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
17440 None - 25 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17464 None - 22 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)