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)KMC
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms28
Net Charge1
Forcefieldmultiple
Molecule ID17442
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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17415 None - 24 1 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17496 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
1564 None - 143 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
1606 None - 20 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
1576 None - 129 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17480 None - 27 -1 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
1540 None - 143 0 Manual* N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17488 None - 21 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
3496 None - 15 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17281 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)