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
Residue Name (RNME)YSU
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-1
Forcefieldmultiple
Molecule ID17477
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 13:07:18
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 
17206 None - 18 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17151 None - 16 -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)