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)DMA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms19
Net Charge0
Forcefieldmultiple
Molecule ID17493
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:18
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 
17473 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 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
1555 None - 167 0 Manual* N/A Compare with
1595 None - 5 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
208 None - 23 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 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
1574 None - 123 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17235 None - 26 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
1553 None - 155 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
568 None - 16 0 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
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17502 None - 32 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)