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)TDH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge0
Forcefieldmultiple
Molecule ID17351
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 13:07:16
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17490 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
17375 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
17466 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
17498 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
17383 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
17474 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
17506 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17391 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
17482 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
6252 None - 89 0 Manual* N/A Compare with
17367 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
17458 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
17192 None - 44 0 Manual N/A Compare with
17431 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
17407 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
17439 None - 25 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17323 None - 18 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17514 None - 26 0 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
17399 None - 21 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17149 None - 16 -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)