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)AMBA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge0
Forcefieldmultiple
Molecule ID1608
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS96 Files

Topology Files Structure Files
GROMOS96 United-Atom MTB

Topology Information

Force Field Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2010-07-20 14:30:41
Literature ReferenceLink

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 
17491 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17541 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
580 None - 12 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17543 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
582 None - 12 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17545 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
584 None - 15 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17547 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
1502 None - 106 0 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17521 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
1507 None - 138 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
562 None - 9 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
565 None - 9 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
567 None - 10 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
569 None - 8 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
573 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17148 None - 33 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)