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) 2000 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)H11
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge-1
Forcefieldmultiple
Molecule ID17275
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:15
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1524 None - 137 0 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 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)