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)P5H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17323
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 (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 
17314 None - 32 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17286 None - 17 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17365 None - 29 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)