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) 2000 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)W6H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms28
Net Charge0
Forcefieldmultiple
Molecule ID17193
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
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 (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 
3488 None - 12 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
30988 None - 1456 0 Template N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17410 None - 18 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17359 None - 30 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17425 None - 34 1 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17221 None - 22 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
18675 None - 140 -3 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
17476 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
5639 None - 127 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
17491 None - 22 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17423 None - 21 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18623 None - 139 -3 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
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17238 None - 16 -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)