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 building block
Residue Name (RNME)RSM
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms32
Net Charge0
Forcefieldmultiple
Molecule ID17314
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 13:07:16
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 
17549 None - 15 -1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17161 None - 23 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17163 None - 23 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
1584 None - 137 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)