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)S1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge-1
Forcefieldmultiple
Molecule ID17369
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 13:07:17
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 
17329 None - 17 -2 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17367 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
17343 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
562 None - 9 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)