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)RMN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms29
Net Charge0
Forcefieldmultiple
Molecule ID17542
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 13:07:19
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 
17260 None - 15 -1 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 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
163 None - 13 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17514 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
171 None - 14 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17522 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
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
203 None - 22 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
1606 None - 20 0 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
17241 None - 26 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
1576 None - 129 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
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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)