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) 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)CYM
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms17
Net Charge0
Forcefieldmultiple
Molecule ID17261
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:15
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 (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms > Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17226 None - 20 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
573 None - 20 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17183 None - 23 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)