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 
4182 None - 5 0 Manual* N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17359 None - 30 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17392 None - 18 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17361 None - 12 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17363 None - 12 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17343 None - 23 -2 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
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
17496 None - 19 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17468 None - 31 0 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
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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)