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 building block
Residue Name (RNME)D1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge-1
Forcefieldmultiple
Molecule ID17180
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17358 None - 30 0 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 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)