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 building block
Residue Name (RNME)L5H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17164
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 13:07:14
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17432 None - 15 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17349 None - 15 0 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17381 None - 23 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1736 None - 80 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)