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)Y2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-2
Forcefieldmultiple
Molecule ID17211
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 13:07:15
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
4908 None - 40 -4 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17455 None - 28 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)