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)S2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms17
Net Charge-2
Forcefieldmultiple
Molecule ID17331
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 
8099 None - 3218 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17392 None - 18 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17170 None - 28 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)