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)MES
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms22
Net Charge0
Forcefieldmultiple
Molecule ID17489
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:18
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 
17359 None - 30 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 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
17494 None - 19 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
4580 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
17410 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
7283 None - 87 1 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
17509 None - 27 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17389 None - 18 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
7281 None - 62 1 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
17507 None - 29 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17268 None - 19 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)