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)P3H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17207
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
3501 None - 21 0 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
1563 None - 137 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17258 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
17324 None - 18 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17241 None - 26 -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)