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 building block
Residue Name (RNME)CAM
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17300
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 13:07:16
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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
3924 None - 176 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17517 None - 28 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17398 None - 21 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 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
17212 None - 27 -2 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17432 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
17195 None - 28 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
580 None - 12 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)