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 
17315 None - 32 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17453 None - 28 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17369 None - 18 -1 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)