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)CSE
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms16
Net Charge-1
Forcefieldmultiple
Molecule ID17151
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 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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17458 None - 28 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17474 None - 23 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17482 None - 15 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17270 None - 18 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17514 None - 26 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17503 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)