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 building block
Residue Name (RNME)YSU
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-1
Forcefieldmultiple
Molecule ID17478
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 13:07:18
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
3410 None - 15 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
1525 None - 147 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)