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) 1000 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)KAL
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge0
Forcefieldmultiple
Molecule ID17421
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS11 Files

Topology Files Structure Files
GROMOS11 United-Atom MTB
United-Atom PDB (optimised geometry)

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:17
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 
17195 None - 28 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
564 None - 6 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)