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)H11
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge-1
Forcefieldmultiple
Molecule ID17275
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 13:07:15
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17162 None - 23 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
17350 None - 15 0 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17382 None - 23 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17175 None - 25 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)