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)RAM
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms32
Net Charge0
Forcefieldmultiple
Molecule ID17503
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 13:07:18
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 
17375 None - 30 -1 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 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
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
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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)