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)D1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge-1
Forcefieldmultiple
Molecule ID17179
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 13:07:14
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 (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 
571 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
178 None - 21 1 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
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
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
17524 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
18622 None - 49 -3 Manual* N/A Compare with
17526 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
18660 None - 49 -3 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17530 None - 18 0 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)