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 building block
Residue Name (RNME)W4H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms28
Net Charge0
Forcefieldmultiple
Molecule ID17518
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 13:07:18
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17425 None - 34 1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17350 None - 15 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17200 None - 26 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)