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)RMC
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms30
Net Charge1
Forcefieldmultiple
Molecule ID17335
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
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 (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 
1547 None - 24 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17523 None - 21 -1 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)