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)CYM
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms17
Net Charge0
Forcefieldmultiple
Molecule ID17261
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 Version54A7 (IFP54A7.dat / 54A7.ifp)
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1679 None - 31 0 Manual* N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17481 None - 15 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17494 None - 19 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
568 None - 16 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)