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)RAM
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms32
Net Charge0
Forcefieldmultiple
Molecule ID17503
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 Version45A3 (IFP45A3.dat)
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 
3486 None - 9 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17340 None - 18 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17190 None - 44 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)