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)K2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-2
Forcefieldmultiple
Molecule ID17247
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 (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 
17455 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
565 None - 9 0 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 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
2919 None - 52 -1 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17167 None - 27 0 Manual N/A Compare with
1587 None - 155 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
177 None - 20 0 Manual* N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
581 None - 16 0 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
1606 None - 20 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
562 None - 9 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
17317 None - 24 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17266 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
1564 None - 143 0 Manual* N/A Compare with
17485 None - 21 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)