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)HTY
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17173
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

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 (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac > Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17264 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
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17196 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
564 None - 6 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
17298 None - 18 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
1771 None - 186 -1 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
1561 None - 119 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)