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)D3H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms16
Net Charge-1
Forcefieldmultiple
Molecule ID17402
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 13:07:17
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1601 None - 17 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17314 None - 32 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17338 None - 18 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
18660 None - 49 -3 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)