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)T2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge-2
Forcefieldmultiple
Molecule ID17346
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 13:07:16
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 
17429 None - 15 0 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17461 None - 22 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17552 None - 15 -1 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)