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)H12
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge-2
Forcefieldmultiple
Molecule ID17249
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 13:07:15
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 
17239 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17413 None - 24 1 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17389 None - 18 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17411 None - 18 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17443 None - 28 1 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17426 None - 34 1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17409 None - 18 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
3924 None - 176 0 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)