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 building block
Residue Name (RNME)CAM
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17300
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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17410 None - 18 0 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17512 None - 27 0 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
2671 None - 47 -3 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)