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)T1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge-1
Forcefieldmultiple
Molecule ID17523
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 13:07:19
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 
1540 None - 143 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17354 None - 23 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17384 None - 23 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
1561 None - 119 0 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17197 None - 26 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)