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)RMS
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms33
Net Charge1
Forcefieldmultiple
Molecule ID17202
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 13:07:14
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 
1511 None - 131 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
1547 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
1587 None - 155 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17340 None - 18 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17535 None - 24 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)