MD Topology | NMR | X-Ray

Visualize with JSmol

Processing Information

QM Processing Stage

Click table to toggle details.

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)HTY
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17173
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 13:07:14
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17307 None - 23 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
3504 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
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1608 None - 20 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
17507 None - 29 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
9643 None - 103 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
17337 None - 18 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
580 None - 12 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
1605 None - 23 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
17505 None - 29 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
9377 None - 12 -2 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
17488 None - 21 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
Previous Page Next Page

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)